Mercurial > repos > nml > quasitools
diff callntvar.xml @ 9:18aad692772a draft default tip
planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
| author | nml |
|---|---|
| date | Mon, 20 Jun 2022 20:06:36 +0000 |
| parents | 9def47f3c1e4 |
| children |
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--- a/callntvar.xml Tue Aug 06 08:50:28 2019 -0400 +++ b/callntvar.xml Mon Jun 20 20:06:36 2022 +0000 @@ -1,12 +1,15 @@ -<tool id="callntvar" name="Nucleotide Variants" version="0.7.0"> +<tool id="callntvar" name="Nucleotide Variants" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description>Identifies nucleotide variants</description> - <requirements> - <requirement type="package" version="0.7.0">quasitools</requirement> - </requirements> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ - ln -f -s ${input_bam.metadata.bam_index} ${input_bam}.bai && - quasitools call ntvar $input_bam $ref_file + ln -s $input_bam '${input_bam.name}' && + ln -s $input_bam.metadata.bam_index '${input_bam.name}.bai' && + + quasitools call ntvar '${input_bam.name}' $ref_file #if $error_rate: -e $error_rate @@ -45,14 +48,5 @@ Call nucleotide variants for a given BAM file and a supplied reference file. ]]></help> - <citations> - <citation type="bibtex"> - @misc{GitHubquasitoolscallntvar, - title = {quasitools callntvar}, - publisher = {phac-nml}, - journal = {GitHub repository}, - url = {https://github.com/phac-nml/quasitools}, - } - </citation> - </citations> + <expand macro="citations" /> </tool>