| Previous changeset 9:c092052ed673 (2021-08-20) Next changeset 11:5671e1d3d5ee (2022-07-13) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 27f076c829f3b79c170cad55fc19e2f48c8b22ed" |
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modified:
ivar_trim.xml |
| b |
| diff -r c092052ed673 -r 9f978da6528a ivar_trim.xml --- 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> |