Mercurial > repos > iuc > ivar_trim

changeset 10:9f978da6528a draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 27f076c829f3b79c170cad55fc19e2f48c8b22ed"
author iuc
date Sun, 20 Mar 2022 11:43:34 +0000
parents c092052ed673
children 5671e1d3d5ee
files ivar_trim.xml
diffstat 1 files changed, 7 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/ivar_trim.xml	Fri Aug 20 20:35:46 2021 +0000
+++ b/ivar_trim.xml	Sun Mar 20 11:43:34 2022 +0000
@@ -1,10 +1,11 @@
-<tool id="ivar_trim" name="ivar trim" version="@VERSION@+galaxy2">
+<tool id="ivar_trim" name="ivar trim" version="@VERSION@+galaxy3">
     <description>Trim reads in aligned BAM</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements">
         <requirement type="package" version="3.8.1">python</requirement>
+        <requirement type="package" version="1.15">samtools</requirement>
     </expand>
     <expand macro="version_command" />
     <command detect_errors="exit_code"><![CDATA[
@@ -14,8 +15,8 @@
             cp '$primer.cached_bed.fields.path' bed.bed &&
         #end if
         python '$__tool_directory__/sanitize_bed.py' bed.bed &&
-        #if $amplicons.filter_by == 'yes' or $amplicons.filter_by == 'yes_computed'
-            #if $amplicons.filter_by == 'yes_computed':
+        #if $amplicons.filter_by == 'yes' or $amplicons.filter_by == 'yes_compute'
+            #if $amplicons.filter_by == 'yes_compute':
                 python '$__tool_directory__/write_amplicon_info_file.py' bed.bed amplicon_info_raw.tsv &&
             #else
                 ln -s '$amplicons.amplicon_info' amplicon_info_raw.tsv &&
@@ -132,6 +133,9 @@
                 <param name="filter_by" value="yes_compute" />
             </conditional>
             <param name="input_bam" value="sars-cov-2/sars_cov2_untrimmed.bam" ftype="bam" />
+            <assert_command>
+                <has_text text="write_amplicon_info_file" />
+            </assert_command>
             <output name="output_bam" file="sars-cov-2/sars_cov2_trimmed.bam" compare="sim_size" delta="100000"/>
         </test>
     </tests>