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bernt-matthiasbernt-matthias
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cnt: make advanced a section
1 parent 26d6f37 commit 48ea3a3

14 files changed

+180
-196
lines changed

‎tests/test-data/bool.xml

Lines changed: 2 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -84,13 +84,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
8484
<param name="sect_flag_true_adv" value="true"/>
8585
<param name="sect_flag_false_adv" value="false"/>
8686
</section>
87-
<conditional name="adv_opts_cond">
87+
<section name="adv_opts">
8888
<param name="true_adv" value="true"/>
8989
<param name="false_adv" value="false"/>
9090
<param name="flag_true_adv" value="true"/>
9191
<param name="flag_false_adv" value="false"/>
92-
<param name="adv_opts_selector" value="advanced"/>
93-
</conditional>
92+
</section>
9493
</test>
9594
</tests>
9695
<help><![CDATA[Bool parameter tests.

‎tests/test-data/empty.xml

Lines changed: 1 addition & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -47,9 +47,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
4747
</outputs>
4848
<tests>
4949
<test expect_num_outputs="1">
50-
<conditional name="adv_opts_cond">
51-
<param name="adv_opts_selector" value="advanced"/>
52-
</conditional>
50+
<section name="adv_opts"/>
5351
</test>
5452
</tests>
5553
<help><![CDATA[empty ctd test

‎tests/test-data/float.xml

Lines changed: 2 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -108,7 +108,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
108108
<param name="sect_default_mandatory_unrestricted_adv_minmax" value="0.0"/>
109109
<param name="sect_default_optional_unrestricted_adv_minmax" value="0.0"/>
110110
</section>
111-
<conditional name="adv_opts_cond">
111+
<section name="adv_opts">
112112
<param name="default_mandatory_unrestricted_adv" value="0.0"/>
113113
<param name="default_optional_unrestricted_adv" value="0.0"/>
114114
<param name="default_mandatory_unrestricted_adv_min" value="0.0"/>
@@ -117,8 +117,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
117117
<param name="default_optional_unrestricted_adv_max" value="0.0"/>
118118
<param name="default_mandatory_unrestricted_adv_minmax" value="0.0"/>
119119
<param name="default_optional_unrestricted_adv_minmax" value="0.0"/>
120-
<param name="adv_opts_selector" value="advanced"/>
121-
</conditional>
120+
</section>
122121
</test>
123122
</tests>
124123
<help><![CDATA[Float parameter tests.

‎tests/test-data/ifile.xml

Lines changed: 141 additions & 142 deletions
Large diffs are not rendered by default.

‎tests/test-data/integer.xml

Lines changed: 2 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -108,7 +108,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
108108
<param name="sect_default_mandatory_unrestricted_adv_minmax" value="0"/>
109109
<param name="sect_default_optional_unrestricted_adv_minmax" value="0"/>
110110
</section>
111-
<conditional name="adv_opts_cond">
111+
<section name="adv_opts">
112112
<param name="default_mandatory_unrestricted_adv" value="0"/>
113113
<param name="default_optional_unrestricted_adv" value="0"/>
114114
<param name="default_mandatory_unrestricted_adv_min" value="0"/>
@@ -117,8 +117,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
117117
<param name="default_optional_unrestricted_adv_max" value="0"/>
118118
<param name="default_mandatory_unrestricted_adv_minmax" value="0"/>
119119
<param name="default_optional_unrestricted_adv_minmax" value="0"/>
120-
<param name="adv_opts_selector" value="advanced"/>
121-
</conditional>
120+
</section>
122121
</test>
123122
</tests>
124123
<help><![CDATA[Integer parameter tests.

‎tests/test-data/label-help.xml

Lines changed: 2 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -79,9 +79,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
7979
<param name="pteg" value="1 2"/>
8080
<param name="coie" value="1 2"/>
8181
<param name="ptie" value="1 2"/>
82-
<conditional name="adv_opts_cond">
83-
<param name="adv_opts_selector" value="advanced"/>
84-
</conditional>
82+
<section name="adv_opts">
83+
</section>
8584
</test>
8685
</tests>
8786
<help><![CDATA[Label Help parameter tests.

‎tests/test-data/ofile-corresponding-input.xml

Lines changed: 1 addition & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -292,9 +292,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
292292
<param name="input_noformat" ftype="txt" value="0test.ext"/>
293293
<param name="input_oneformat" ftype="tsv" value="1test.ext"/>
294294
<param name="input_multformat" ftype="tabular" value="2test.ext"/>
295-
<conditional name="adv_opts_cond">
296-
<param name="adv_opts_selector" value="advanced"/>
297-
</conditional>
295+
<section name="adv_opts"/>
298296
<output name="mandatory_noformat" ftype="txt" value="outfile.txt"/>
299297
<output name="mandatory_oneformat" ftype="tsv" value="outfile.txt"/>
300298
<output name="mandatory_multformat" value="outfile.txt"/>

‎tests/test-data/ofile-mult-typeparam.xml

Lines changed: 1 addition & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -90,8 +90,7 @@ ${' '.join(["&& mv -n 'test_section_sect_mandatory_mandatoryinput/%(bn)s/%(id)s.
9090
<param name="sect_mandatory_mandatoryinput_type" value="eut"/>
9191
<param name="sect_inp_mandatory_mandatoryinput" ftype="tsv" value="1test.ext,1test2.ext"/>
9292
</section>
93-
<conditional name="adv_opts_cond">
94-
<param name="adv_opts_selector" value="advanced"/>
93+
<conditional name="adv_opts">
9594
</conditional>
9695
<output_collection name="mandatory_mandatoryinput" count="0"/>
9796
<output_collection name="test_section_sect_mandatory_mandatoryinput" count="0"/>

‎tests/test-data/ofile-mult.xml

Lines changed: 2 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -84,9 +84,8 @@ ${' '.join(["&& mv -n 'mandatory_mandatoryinput/%(bn)s/%(id)s.%(gext)s' 'mandato
8484
<test expect_num_outputs="1">
8585
<param name="inp_mandatory_mandatoryinput" ftype="tsv" value="0test.ext,0test2.ext"/>
8686
<param name="inp_optional_mandatoryinput" ftype="tsv" value="1test.ext,1test2.ext"/>
87-
<conditional name="adv_opts_cond">
88-
<param name="adv_opts_selector" value="advanced"/>
89-
</conditional>
87+
<section name="adv_opts">
88+
</section>
9089
<output_collection name="mandatory_mandatoryinput" count="0"/>
9190
</test>
9291
</tests>

‎tests/test-data/ofile-typeparam.xml

Lines changed: 10 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -84,10 +84,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
8484
'optional_noformat_adv/output.${gxy2omsext("txt")}'
8585
#end if
8686
-mandatory_multformat_adv
87-
'mandatory_multformat_adv/output.${adv_opts_cond.mandatory_multformat_adv_type}'
87+
'mandatory_multformat_adv/output.${adv_opts.mandatory_multformat_adv_type}'
8888
#if "optional_multformat_adv_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
8989
-optional_multformat_adv
90-
'optional_multformat_adv/output.${adv_opts_cond.optional_multformat_adv_type}'
90+
'optional_multformat_adv/output.${adv_opts.optional_multformat_adv_type}'
9191
#end if
9292
-decoy_input_noformat
9393
'decoy_input_noformat/${re.sub("[^\w\-_]", "_", $decoy_input_noformat.element_identifier)}.$gxy2omsext($decoy_input_noformat.ext)'
@@ -142,9 +142,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
142142
#if "optional_noformat_adv_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
143143
&& mv 'optional_noformat_adv/output.${gxy2omsext("txt")}' '$optional_noformat_adv'
144144
#end if
145-
&& mv 'mandatory_multformat_adv/output.${adv_opts_cond.mandatory_multformat_adv_type}' '$mandatory_multformat_adv'
145+
&& mv 'mandatory_multformat_adv/output.${adv_opts.mandatory_multformat_adv_type}' '$mandatory_multformat_adv'
146146
#if "optional_multformat_adv_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
147-
&& mv 'optional_multformat_adv/output.${adv_opts_cond.optional_multformat_adv_type}' '$optional_multformat_adv'
147+
&& mv 'optional_multformat_adv/output.${adv_opts.optional_multformat_adv_type}' '$optional_multformat_adv'
148148
#end if
149149
&& mv 'test_section_sect_mandatory_noformat/output.${gxy2omsext("txt")}' '$test_section_sect_mandatory_noformat'
150150
#if "sect_optional_noformat_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
@@ -312,14 +312,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
312312
</data>
313313
<data name="mandatory_multformat_adv" label="${tool.name} on ${on_string}: mandatory_multformat_adv" format="tsv">
314314
<change_format>
315-
<when input="adv_opts_cond.mandatory_multformat_adv_type" value="eyt" format="tabular"/>
316-
<when input="adv_opts_cond.mandatory_multformat_adv_type" value="ezt" format="tabular"/>
315+
<when input="adv_opts.mandatory_multformat_adv_type" value="eyt" format="tabular"/>
316+
<when input="adv_opts.mandatory_multformat_adv_type" value="ezt" format="tabular"/>
317317
</change_format>
318318
</data>
319319
<data name="optional_multformat_adv" label="${tool.name} on ${on_string}: optional_multformat_adv" format="tsv">
320320
<change_format>
321-
<when input="adv_opts_cond.optional_multformat_adv_type" value="eyt" format="tabular"/>
322-
<when input="adv_opts_cond.optional_multformat_adv_type" value="ezt" format="tabular"/>
321+
<when input="adv_opts.optional_multformat_adv_type" value="eyt" format="tabular"/>
322+
<when input="adv_opts.optional_multformat_adv_type" value="ezt" format="tabular"/>
323323
</change_format>
324324
<filter>OPTIONAL_OUTPUTS is not None and "optional_multformat_adv_FLAG" in OPTIONAL_OUTPUTS</filter>
325325
</data>
@@ -383,13 +383,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
383383
<param name="sect_decoy_input_oneformat" ftype="tsv" value="4test.ext"/>
384384
<param name="sect_decoy_input_multformat" ftype="tabular" value="5test.ext"/>
385385
</section>
386-
<conditional name="adv_opts_cond">
386+
<section name="adv_opts">
387387
<param name="mandatory_noformat_adv_type" value="ext"/>
388388
<param name="optional_noformat_adv_type" value="ext"/>
389389
<param name="mandatory_multformat_adv_type" value="ext"/>
390390
<param name="optional_multformat_adv_type" value="ext"/>
391-
<param name="adv_opts_selector" value="advanced"/>
392-
</conditional>
391+
</section>
393392
<output name="mandatory_noformat" ftype="txt" value="outfile.txt"/>
394393
<output name="mandatory_multformat" ftype="tsv" value="outfile.txt"/>
395394
<output name="mandatory_noformat_adv" ftype="txt" value="outfile.txt"/>

‎tests/test-data/ofile.xml

Lines changed: 10 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -100,10 +100,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
100100
'optional_oneformat_adv/output.${gxy2omsext("tsv")}'
101101
#end if
102102
-mandatory_multformat_adv
103-
'mandatory_multformat_adv/output.${adv_opts_cond.mandatory_multformat_adv_type}'
103+
'mandatory_multformat_adv/output.${adv_opts.mandatory_multformat_adv_type}'
104104
#if "optional_multformat_adv_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
105105
-optional_multformat_adv
106-
'optional_multformat_adv/output.${adv_opts_cond.optional_multformat_adv_type}'
106+
'optional_multformat_adv/output.${adv_opts.optional_multformat_adv_type}'
107107
#end if
108108
-test_section:sect_mandatory_noformat
109109
'test_section_sect_mandatory_noformat/output.${gxy2omsext("txt")}'
@@ -166,9 +166,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
166166
#if "optional_oneformat_adv_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
167167
&& mv 'optional_oneformat_adv/output.${gxy2omsext("tsv")}' '$optional_oneformat_adv'
168168
#end if
169-
&& mv 'mandatory_multformat_adv/output.${adv_opts_cond.mandatory_multformat_adv_type}' '$mandatory_multformat_adv'
169+
&& mv 'mandatory_multformat_adv/output.${adv_opts.mandatory_multformat_adv_type}' '$mandatory_multformat_adv'
170170
#if "optional_multformat_adv_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
171-
&& mv 'optional_multformat_adv/output.${adv_opts_cond.optional_multformat_adv_type}' '$optional_multformat_adv'
171+
&& mv 'optional_multformat_adv/output.${adv_opts.optional_multformat_adv_type}' '$optional_multformat_adv'
172172
#end if
173173
&& mv 'test_section_sect_mandatory_noformat/output.${gxy2omsext("txt")}' '$test_section_sect_mandatory_noformat'
174174
#if "sect_optional_noformat_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
@@ -294,14 +294,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
294294
</data>
295295
<data name="mandatory_multformat_adv" label="${tool.name} on ${on_string}: mandatory_multformat_adv" format="tsv">
296296
<change_format>
297-
<when input="adv_opts_cond.mandatory_multformat_adv_type" value="eyt" format="tabular"/>
298-
<when input="adv_opts_cond.mandatory_multformat_adv_type" value="ezt" format="tabular"/>
297+
<when input="adv_opts.mandatory_multformat_adv_type" value="eyt" format="tabular"/>
298+
<when input="adv_opts.mandatory_multformat_adv_type" value="ezt" format="tabular"/>
299299
</change_format>
300300
</data>
301301
<data name="optional_multformat_adv" label="${tool.name} on ${on_string}: optional_multformat_adv" format="tsv">
302302
<change_format>
303-
<when input="adv_opts_cond.optional_multformat_adv_type" value="eyt" format="tabular"/>
304-
<when input="adv_opts_cond.optional_multformat_adv_type" value="ezt" format="tabular"/>
303+
<when input="adv_opts.optional_multformat_adv_type" value="eyt" format="tabular"/>
304+
<when input="adv_opts.optional_multformat_adv_type" value="ezt" format="tabular"/>
305305
</change_format>
306306
<filter>OPTIONAL_OUTPUTS is not None and "optional_multformat_adv_FLAG" in OPTIONAL_OUTPUTS</filter>
307307
</data>
@@ -361,11 +361,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
361361
<param name="sect_mandatory_multformat_adv_type" value="ext"/>
362362
<param name="sect_optional_multformat_adv_type" value="ext"/>
363363
</section>
364-
<conditional name="adv_opts_cond">
364+
<section name="adv_opts">
365365
<param name="mandatory_multformat_adv_type" value="ext"/>
366366
<param name="optional_multformat_adv_type" value="ext"/>
367-
<param name="adv_opts_selector" value="advanced"/>
368-
</conditional>
367+
</section>
369368
<output name="mandatory_noformat" ftype="txt" value="outfile.txt"/>
370369
<output name="mandatory_oneformat" ftype="tsv" value="outfile.txt"/>
371370
<output name="mandatory_multformat" ftype="tsv" value="outfile.txt"/>

‎tests/test-data/repeat_test.xml

Lines changed: 2 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -449,7 +449,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
449449
<param name="sect_double_resticted_default_optional_adv" value="-0.3 0.5"/>
450450
<param name="sect_double_resticted_default_mandatory_adv" value="-0.3 0.5"/>
451451
</section>
452-
<conditional name="adv_opts_cond">
452+
<section name="adv_opts">
453453
<param name="string_wodefault_mandatory_adv" value="1 2"/>
454454
<param name="string_default_optional_adv" value="&quot;A A&quot; -B"/>
455455
<param name="string_default_mandatory_adv" value="&quot;A A&quot; -B"/>
@@ -465,8 +465,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
465465
<param name="double_resticted_wodefault_mandatory_adv" value="1 2"/>
466466
<param name="double_resticted_default_optional_adv" value="-0.3 0.5"/>
467467
<param name="double_resticted_default_mandatory_adv" value="-0.3 0.5"/>
468-
<param name="adv_opts_selector" value="advanced"/>
469-
</conditional>
468+
</section>
470469
</test>
471470
</tests>
472471
<help><![CDATA[Repeat parameter tests.

‎tests/test-data/select_test.xml

Lines changed: 2 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -544,13 +544,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
544544
<param name="sect_list_wodefault_mandatory_adv" value="A,B,C,D"/>
545545
<param name="sect_list_wodefault_mandatory_many_adv" value="A,B,C,D,E"/>
546546
</section>
547-
<conditional name="adv_opts_cond">
547+
<section name="adv_opts">
548548
<param name="wodefault_mandatory_adv" value="A"/>
549549
<param name="wodefault_mandatory_many_adv" value="A"/>
550550
<param name="list_wodefault_mandatory_adv" value="A,B,C,D"/>
551551
<param name="list_wodefault_mandatory_many_adv" value="A,B,C,D,E"/>
552-
<param name="adv_opts_selector" value="advanced"/>
553-
</conditional>
552+
</section>
554553
</test>
555554
</tests>
556555
<help><![CDATA[Select parameter tests.

‎tests/test-data/string.xml

Lines changed: 2 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -109,12 +109,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
109109
<param name="sect_default_mandatory_unrestricted_adv" value="default"/>
110110
<param name="sect_default_optional_unrestricted_adv" value="default"/>
111111
</section>
112-
<conditional name="adv_opts_cond">
112+
<section name="adv_opts">
113113
<param name="wodefault_mandatory_unrestricted_adv" value="1 2"/>
114114
<param name="default_mandatory_unrestricted_adv" value="default"/>
115115
<param name="default_optional_unrestricted_adv" value="default"/>
116-
<param name="adv_opts_selector" value="advanced"/>
117-
</conditional>
116+
</section>
118117
</test>
119118
</tests>
120119
<help><![CDATA[String parameter tests.

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