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comparison ivar_trim.xml @ 22:6606a8c97889 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 97f230215d53e71748c78cd21633d92143710b94
author iuc
date Wed, 06 Aug 2025 08:21:20 +0000
parents c9ef01b1cfba
children
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21:7bd020da0ce5 22:6606a8c97889
1 <tool id="ivar_trim" name="ivar trim" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> 1 <tool id="ivar_trim" name="ivar trim" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
2 <description>Trim reads in aligned BAM</description> 2 <description>Trim reads in aligned BAM</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="xrefs"/> 6 <expand macro="xrefs"/>
7 <expand macro="requirements"/> 7 <expand macro="requirements">
8 <requirement type="package" version="0.1.0">viramp-hub</requirement>
9 </expand>
8 <expand macro="version_command"/> 10 <expand macro="version_command"/>
9 <command detect_errors="exit_code"><![CDATA[ 11 <command detect_errors="exit_code"><![CDATA[
12 ## Prepare primer scheme and, if necessary, also amplicon info file
10 #if $primer.source == 'history' 13 #if $primer.source == 'history'
11 cp '$primer.input_bed' bed.bed && 14 ln -s '$primer.input_bed' bed.bed &&
12 #else 15 #else
13 cp '$primer.cached_bed.fields.path' bed.bed && 16 ln -s '$primer.cached_bed.fields.path' bed.bed &&
14 #end if 17 #end if
15 python '$__tool_directory__/sanitize_bed.py' bed.bed && 18 scheme-convert --to bed --bed-type ivar -o ivar.bed bed.bed &&
16 #if $amplicons.filter_by == 'yes' or $amplicons.filter_by == 'yes_compute' 19 #if $amplicons.filter_by == 'yes_compute':
17 #if $amplicons.filter_by == 'yes_compute': 20 scheme-convert --to amplicon-info -r outer -o amplicon_info.tsv ivar.bed &&
18 python '$__tool_directory__/write_amplicon_info_file.py' bed.bed amplicon_info_raw.tsv && 21 #elif $amplicons.filter_by == 'yes':
19 #else 22 ## just check the amplicon info file against the primer scheme and reduce it to its outer primers
20 ln -s '$amplicons.amplicon_info' amplicon_info_raw.tsv && 23 scheme-convert -a '$amplicons.amplicon_info' --to amplicon-info -r outer -o amplicon_info.tsv ivar.bed &&
21 #end if
22 python '$__tool_directory__/prepare_amplicon_info.py' bed.bed amplicon_info_raw.tsv amplicon_info.tsv &&
23 #end if 24 #end if
24 ln -s '$input_bam' sorted.bam && 25 ln -s '$input_bam' sorted.bam &&
25 ln -s '${input_bam.metadata.bam_index}' sorted.bam.bai && 26 ln -s '${input_bam.metadata.bam_index}' sorted.bam.bai &&
26 27
27 ivar trim 28 ivar trim
28 -i sorted.bam 29 -i sorted.bam
29 -b bed.bed 30 -b ivar.bed
30 #if $amplicons.filter_by == 'yes' or $amplicons.filter_by == 'yes_compute' 31 #if $amplicons.filter_by == 'yes' or $amplicons.filter_by == 'yes_compute'
31 -f amplicon_info.tsv 32 -f amplicon_info.tsv
32 #end if 33 #end if
33 -x $primer_pos_wiggle 34 -x $primer_pos_wiggle
34 $inc_primers 35 $inc_primers
111 <output name="output_bam" file="covid19/PC00101P_sub.sorted.bam" compare="sim_size" delta="300000"/> 112 <output name="output_bam" file="covid19/PC00101P_sub.sorted.bam" compare="sim_size" delta="300000"/>
112 </test> 113 </test>
113 <test> 114 <test>
114 <!-- Test with primer bed file that needs to be sanitized --> 115 <!-- Test with primer bed file that needs to be sanitized -->
115 <param name="input_bam" value="covid19/PC00101P_sub.sorted.bam" /> 116 <param name="input_bam" value="covid19/PC00101P_sub.sorted.bam" />
116 <param name="input_bed" value="covid19/ARTIC-V1-bad.bed" /> 117 <param name="input_bed" ftype="bed" value="covid19/ARTIC-V1-bad.bed" />
117 <param name="inc_primers" value="true" /> 118 <param name="inc_primers" value="true" />
118 <conditional name="trimmed_length"> 119 <conditional name="trimmed_length">
119 <param name="filter" value="custom" /> 120 <param name="filter" value="custom" />
120 <param name="min_len" value="30" /> 121 <param name="min_len" value="30" />
121 </conditional> 122 </conditional>
178 <conditional name="trimmed_length"> 179 <conditional name="trimmed_length">
179 <param name="filter" value="custom" /> 180 <param name="filter" value="custom" />
180 <param name="min_len" value="30" /> 181 <param name="min_len" value="30" />
181 </conditional> 182 </conditional>
182 <assert_command> 183 <assert_command>
183 <has_text text="write_amplicon_info_file" /> 184 <has_text text="scheme-convert --to amplicon-info -r outer" />
184 </assert_command> 185 </assert_command>
185 <output name="output_bam" file="sars-cov-2/sars_cov2_trimmed.bam" compare="sim_size" delta="100000"/> 186 <output name="output_bam" file="sars-cov-2/sars_cov2_trimmed.bam" compare="sim_size" delta="100000"/>
186 </test> 187 </test>
187 </tests> 188 </tests>
188 <help><![CDATA[ 189 <help><![CDATA[