Adding a new tool: read2tree #7318
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| remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/main/tools/read2tree | ||
| categories: | ||
| - "Genomics Analysis" No newline at end of file |
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You need to use one of the categories of the toolshed.
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| <tool id="read2tree" name="Read2Tree" version="2.0.1" python_template_version="3.5"> | |||
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Can you use a TOOL_VERSION macro for the version? Like here: https://github.com/galaxyproject/tools-iuc/blob/main/tools/berokka/berokka.xml
| rm -rf ./genes_dir; | ||
| rm -rf ./output; |
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This should not be needed. Every jobs gets a fresh working dir.
| #set $i = 0 | ||
| #for $f in $marker_genes | ||
| #set $i = $i + 1 |
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| #set $i = 0 | |
| #for $f in $marker_genes | |
| #set $i = $i + 1 | |
| #for $i, $f in enumerate($marker_genes) |
| #set $i = 0 | ||
| #for $f in $marker_genes | ||
| #set $i = $i + 1 | ||
| ln -s -- `readlink -f $f` "./genes_dir/$i".fa; |
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| ln -s -- `readlink -f $f` "./genes_dir/$i".fa; | |
| ln -s '$f' "./genes_dir/$i".fa; |
| ]]></command> | ||
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| <inputs> | ||
| <param name="reads" type="data" multiple="true" format="fasta,fastq" label="Input reads in FASTA or FASTQ" |
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Use fastqsanger and/or fastqillumina instead of fastq.
Does the software accept gzipped data?
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| <!--param name="marker_genes" type="data" multiple="true" format="fasta" label="Marker genes"/--> | ||
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| <param name="marker_genes" type="data_collection" collection_type="list" |
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You could also use a data parameter with multiple="true". Users can still use collections. But there might be good reason for using a acollection?
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marker genes could be dozens or more files. I figured it's easier to upload them and build into a collection first than do multiple="true". Otherwise on the tool page the user has to select all them one by one again
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If you look at the tool form there are a few buttons left of the data selector (for data inputs with multiple="true")
Multiple datasets: the user can select multiple datasetsDataset collectionthe user can select a collection
That is collection input also works in this case. The only downside is that the element_identifiers are not really useful for users choosing option 1.
I'm completely fine with collection input. Just wanted to make you aware.
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| <tests> | ||
| <test> | ||
| <param name="reads" value="sample_1.fastq,sample_2.fastq"/> |
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Guess the fastq files could be downsampled to reduce size?
| <param name="marker_genes" type="data_collection" collection_type="list" | ||
| label="Marker gene files" help="A set of reference orthologous groups, i.e. marker genes. See https://github.com/DessimozLab/read2tree for detail."/> | ||
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| <param name="dna_ref" type="data" format="fasta" label="DNA reference" |
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This seems to be optional? Could you add a few words to the help when this is needed and what it is?
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| <tool id="read2tree" name="Read2Tree" version="2.0.1" python_template_version="3.5"> | |||
| <param name="marker_genes" type="data_collection" collection_type="list" | ||
| label="Marker gene files" help="A set of reference orthologous groups, i.e. marker genes. See https://github.com/DessimozLab/read2tree for detail."/> | ||
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| <param name="dna_ref" type="data" format="fasta" label="DNA reference" |
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Can you use the argument attribute instead of (or in addition to) name
| </param> | ||
| <param name="dna_ref" value="dna_ref.fa"/> | ||
| <output name="output_tree"> | ||
| <assert_contents> |
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maybe making this test a bit more stricter? For example by asserting the line count?
3 participants
FOR CONTRIBUTOR:
As the title says, this request adds read2tree.