Mercurial > repos > iuc > mykrobe_predict
changeset 3:e8405163fb4e draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 2b9fb5d1f0ffb7ecd51561d3e325813c4f8e7f3e"
| author | iuc |
|---|---|
| date | Tue, 10 Aug 2021 11:29:58 +0000 |
| parents | cedd631dc124 |
| children | a2e3ad69ee23 |
| files | macro.xml mykrobe_predict.xml test-data/reads.fastq.gz |
| diffstat | 3 files changed, 54 insertions(+), 62 deletions(-) [+] |
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--- a/macro.xml Thu Jan 02 12:03:50 2020 -0500 +++ b/macro.xml Tue Aug 10 11:29:58 2021 +0000 @@ -1,40 +1,14 @@ <?xml version="1.1"?> <macros> + <token name="@TOOL_VERSION@">0.10.0</token> <xml name="requirements"> <requirements> - <requirement type="package" version="0.7.0">mykrobe</requirement> + <requirement type="package" version="@TOOL_VERSION@">mykrobe</requirement> </requirements> </xml> <token name="@select_inputs@"> <![CDATA[ #set $name='sample' - #set $type='fastq' - ## Adding sample name, indicate specie and inputs fastq(s) files - #if $data_type.type == "paired": - - ln -s '$data_type.fastq_input1' sample_1.fastq && - ln -s '$data_type.fastq_input2' sample_2.fastq && - - - #elif $data_type.type == "collection": - #set $name=str($data_type.fastq_input1.name) - ln -s '$data_type.fastq_input1.forward' '$data_type.fastq_input1.name'_1.fastq && - ln -s '$data_type.fastq_input1.reverse' '$data_type.fastq_input1.name'_2.fastq && - - #elif $data_type.type == "single": - - - #if $data_type.fastq_input1.is_of_type('fastqsanger') or $data_type.fastq_input1.is_of_type('fastq'): - ln -s '$data_type.fastq_input1' sample.fastq && - - #end if - - #if $data_type.fastq_input1.is_of_type('bam'): - ln -s '$data_type.fastq_input1' sample.bam && - #set $type='bam' - #end if - - #end if ]]> </token> @@ -97,14 +71,14 @@ <option value="collection">Collection Paired-end Data</option> </param> <when value="single"> - <param name="fastq_input1" type="data" format="fastqsanger, fastq,fasta,bam" label="Single end read file(s)"/> + <param name="seq1" type="data" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz,fasta,fasta.gz,bam" label="Single end read file(s)"/> </when> <when value="paired"> - <param name="fastq_input1" type="data" format="fastqsanger, fastq" label="Forward paired-end read file"/> - <param name="fastq_input2" type="data" format="fastqsanger, fastq" label="Reverse paired-end read file"/> + <param name="seq1" type="data" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz" label="Forward paired-end read file"/> + <param name="seq2" type="data" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz" label="Reverse paired-end read file"/> </when> <when value="collection"> - <param name="fastq_input1" type="data_collection" label="Paired-end reads collection" optional="false" format="fastqsanger, fastq" collection_type="paired" /> + <param name="collection1" type="data_collection" label="Paired-end reads collection" optional="false" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz" collection_type="paired" /> </when> </conditional> </xml>
--- a/mykrobe_predict.xml Thu Jan 02 12:03:50 2020 -0500 +++ b/mykrobe_predict.xml Tue Aug 10 11:29:58 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="mykrobe_predict" name="mkyrobe predict" version="0.7.0"> +<tool id="mykrobe_predict" name="mkyrobe predict" version="@TOOL_VERSION@"> <description>Antibiotic resistance predictions</description> <macros> <import>macro.xml</import> @@ -9,19 +9,9 @@ @select_inputs@ mykrobe predict - '${name}' - ${select_species.species} - - #if $select_species.panel == 'custom': - #if $adv.custom_probe: - --custom_probe_set_path '${adv.custom_probe}' - #end if - #if $adv.custom_variant_to_resistance: - --custom_variant_to_resistance_json '${adv.custom_variant_to_resistance}' - #end if - #elif $select_species.panel: - --panel '${select_species.panel}' - #end if + --sample '${name}' + --species ${select_species.species} + --panel '${select_species.panel}' #if $conf_percent_cutoff: --conf_percent_cutoff '${conf_percent_cutoff}' @@ -36,12 +26,14 @@ -q -t "\${GALAXY_SLOTS:-1}" - -1 - #if $type == 'fastq': - *.fastq - #else - *.bam - #end if + --seq + #if $data_type.type == "single": + $data_type.seq1 + #elif $data_type.type == "paired": + $data_type.seq1 $data_type.seq2 + #elif $data_type.type == "collection": + $data_type.collection1.forward $data_type.collection1.reverse + #end if --format '${format}' @@ -54,25 +46,27 @@ <param name="species" type="select" label="Specify Species for AMR"> <option value="tb">Mycobacterium tuberculosis (tb)</option> <option value="staph">Staphylococcus aureus (staph)</option> + <option value="sonnei">Shigella sonnei (sonnei)</option> </param> <when value="staph"> - <param name="panel" type="select" optional="true" label="Select panel for Staph only"> - <option value="custom">Custom</option> + <param name="panel" type="select" label="Select panel for Staph only"> + <option value="20170217">20170217</option> </param> </when> <when value="tb"> - <param name="panel" type="select" label="Select panel for TB only"> + <param name="panel" type="select" label="Select panel for TB only"> + <option value="202010">202010</option> <option value="201901">201901</option> <option value="bradley-2015">Bradely 2015</option> - <option value="walker-2015">Walker 2015</option> - <option value="custom">Custom</option> + </param> + </when> + <when value="sonnei"> + <param name="panel" type="select" label="Select panel for sonnei only"> + <option value="20210201">20210201</option> + <option value="20201012">20201012</option> </param> </when> </conditional> - <section name="adv" title="Custom Panel" expanded="false"> - <param name="custom_probe" type="data" format="fasta" label="Custom Probe" optional="True" help="Don't include filtered genotypes"/> - <param name="custom_variant_to_resistance" type="data" format="json" label="Custom Variant to Resistance" optional="True" help="JSON file with key,value pairs of variant names and induced drug resistance."/> - </section> <param argument="--min_depth" optional="True" type="integer" min="0" label="Minimum depth" help=""/> <param argument="--conf_percent_cutoff" optional="True" type="integer" label="Confidence percent cutoff" help="Number between 0 and 100. Determines --min_variant_conf, by simulating variants and choosing the cutoff that would keep x% of the variants. Default is 90 if --ont, otherwise --min_variant_conf is used as the cutoff"> <validator type="in_range" min="0" max="100" message="Confidence percent cutoff should be between 0 and 100" /> @@ -93,7 +87,7 @@ <tests> <test> <param name="type" value="single"/> - <param name="fastq_input1" value="reads.fastq"/> + <param name="seq1" ftype="fastq" value="reads.fastq"/> <param name="species" value="tb"/> <param name="panel" value="bradley-2015"/> <param name="format" value="json"/> @@ -103,6 +97,30 @@ </assert_contents> </output> </test> + <test> + <param name="type" value="single"/> + <param name="seq1" ftype="fastq" value="reads.fastq"/> + <param name="species" value="sonnei"/> + <param name="panel" value="20201012"/> + <param name="format" value="json"/> + <output name="output"> + <assert_contents> + <has_text_matching expression="susceptibility"/> + </assert_contents> + </output> + </test> + <test> + <param name="type" value="single"/> + <param name="seq1" ftype="fastq.gz" value="reads.fastq.gz"/> + <param name="species" value="sonnei"/> + <param name="panel" value="20201012"/> + <param name="format" value="json"/> + <output name="output"> + <assert_contents> + <has_text_matching expression="susceptibility"/> + </assert_contents> + </output> + </test> </tests> <help> @ATTRIBUTION@