Mercurial > repos > iuc > biotradis
changeset 2:d1278922a88e draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 6a29aaead9d6b0f69ef70113df58047877fc6ce5"
| author | iuc |
|---|---|
| date | Wed, 04 Nov 2020 15:32:21 +0000 |
| parents | e8cb43bd2fe4 |
| children | 476d4cefec3a |
| files | bacteria_tradis.xml tradis_essentiality.xml tradis_gene_insert_sites.xml |
| diffstat | 3 files changed, 8 insertions(+), 12 deletions(-) [+] |
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--- a/bacteria_tradis.xml Fri Feb 07 10:20:18 2020 +0000 +++ b/bacteria_tradis.xml Wed Nov 04 15:32:21 2020 +0000 @@ -4,7 +4,7 @@ <import>macros.xml</import> </macros> <expand macro="requirements" /> - <command> + <command detect_errors="aggressive"> <![CDATA[ ls '${input_fastq}' > file.txt && bacteria_tradis -v -f file.txt -r '${input_ref}'
--- a/tradis_essentiality.xml Fri Feb 07 10:20:18 2020 +0000 +++ b/tradis_essentiality.xml Wed Nov 04 15:32:21 2020 +0000 @@ -4,25 +4,21 @@ <import>macros.xml</import> </macros> <expand macro="requirements" /> - <command> + <command detect_errors="aggressive"> <![CDATA[ ln -s '$input_insert_file' input.csv && - tradis_essentiality.R input.csv + tradis_essentiality.R input.csv ]]> </command> - <inputs> <param name="input_insert_file" type="data" format="csv" label="Gene insertion counts" help="Ourput file of `Bio-TraDis counts to gene insertion data` tool"/> </inputs> - <outputs> - - <data name="ess_genes" format="csv" label="${tool.name} on ${on_string} : Essential genes" from_work_dir="input.csv.essen.csv"/> - <data name="ambig_genes" format="csv" label="${tool.name} on ${on_string} : Unclassified genes" from_work_dir="input.csv.ambig.csv"/> - <data name="all_genes" format="csv" label="${tool.name} on ${on_string} : All genes" from_work_dir="input.csv.all.csv"/> - <data name="qc_results" format="pdf" label="${tool.name} on ${on_string} : QC report" from_work_dir="input.csv.QC_and_changepoint_plots.pdf"/> + <data name="ess_genes" format="csv" label="${tool.name} on ${on_string}: Essential genes" from_work_dir="input.csv.essen.csv"/> + <data name="ambig_genes" format="csv" label="${tool.name} on ${on_string}: Unclassified genes" from_work_dir="input.csv.ambig.csv"/> + <data name="all_genes" format="csv" label="${tool.name} on ${on_string}: All genes" from_work_dir="input.csv.all.csv"/> + <data name="qc_results" format="pdf" label="${tool.name} on ${on_string}: QC report" from_work_dir="input.csv.QC_and_changepoint_plots.pdf"/> </outputs> - <tests> <test> <param name="input_insert_file" ftype="csv" value="test.csv"/>
--- a/tradis_gene_insert_sites.xml Fri Feb 07 10:20:18 2020 +0000 +++ b/tradis_gene_insert_sites.xml Wed Nov 04 15:32:21 2020 +0000 @@ -4,7 +4,7 @@ <import>macros.xml</import> </macros> <expand macro="requirements" /> - <command> + <command detect_errors="aggressive"> <![CDATA[ tradis_gene_insert_sites -trim3 '$trim3' -trim5 '$trim5' '$input_annot' '$input_counts' ]]>