Mercurial > repos > iuc > ivar_trim
diff ivar_trim.xml @ 4:db536ad45f28 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6"
| author | iuc |
|---|---|
| date | Mon, 22 Jun 2020 07:30:46 -0400 |
| parents | 5d6ed46cc101 |
| children | cf65217ad61c |
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--- a/ivar_trim.xml Fri Jun 05 04:12:52 2020 -0400 +++ b/ivar_trim.xml Mon Jun 22 07:30:46 2020 -0400 @@ -1,17 +1,23 @@ -<tool id="ivar_trim" name="ivar trim" version="@VERSION@+galaxy0"> +<tool id="ivar_trim" name="ivar trim" version="@VERSION@+galaxy1"> <description>Trim reads in aligned BAM</description> <macros> <import>macros.xml</import> </macros> - <expand macro="requirements" /> + <expand macro="requirements"> + <requirement type="package" version="3.8.1">python</requirement> + </expand> <expand macro="version_command" /> <command detect_errors="exit_code"><![CDATA[ #if $primer.source == "history" - ln -s '$primer.input_bed' bed.bed && + cp '$primer.input_bed' bed.bed && #else - ln -s '$primer.cached_bed.fields.path' bed.bed && - #end if + cp '$primer.cached_bed.fields.path' bed.bed && + #end if + python '$__tool_directory__/sanitize_bed.py' bed.bed && + ln -s '$input_bam' sorted.bam && + ln -s '${input_bam.metadata.bam_index}' sorted.bam.bai && + ivar trim -i sorted.bam -b bed.bed @@ -57,6 +63,13 @@ <param name="inc_primers" value="true" /> <output name="output_bam" file="covid19/PC00101P_sub.sorted.bam" compare="sim_size" delta="300000"/> </test> + <test> + <!-- Test with primer bed file that needs to be sanitized --> + <param name="input_bam" value="covid19/PC00101P_sub.sorted.bam" /> + <param name="input_bed" value="covid19/ARTIC-V1-bad.bed" /> + <param name="inc_primers" value="true" /> + <output name="output_bam" file="covid19/PC00101P_sub.sorted.bam" compare="sim_size" delta="300000"/> + </test> <!-- #1: Zika data--> <test> <conditional name="primer">