Mercurial > repos > bgruening > trim_galore

comparison trim_galore.xml @ 13:b6c00b82f623 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit be11349529528f508eb05073396e80c3d1cbed4d
author bgruening
date Thu, 01 Jun 2017 08:59:04 -0400
parents 1bf4789584dc
children 949f01671246
comparison
equal deleted inserted replaced
12:1bf4789584dc 13:b6c00b82f623
1 <tool id="trim_galore" name="Trim Galore!" version="0.4.3.0" profile="17.01"> 1 <tool id="trim_galore" name="Trim Galore!" version="0.4.3.1" profile="17.01">
2 <!-- Wrapper compatible with Trim Galore! version 0.4.3 --> 2 <!-- Wrapper compatible with Trim Galore! version 0.4.3 -->
3 <description>Quality and adapter trimmer of reads</description> 3 <description>Quality and adapter trimmer of reads</description>
4 <macros> 4 <macros>
5 <macro name="adapter_trimming"> 5 <macro name="adapter_trimming">
6 <conditional name="trimming"> 6 <conditional name="trimming">
46 <requirement type="package" version="0.4.3">trim-galore</requirement> 46 <requirement type="package" version="0.4.3">trim-galore</requirement>
47 </requirements> 47 </requirements>
48 <version_command> 48 <version_command>
49 trim_galore --version 49 trim_galore --version
50 </version_command> 50 </version_command>
51 <command detect_errors="exit_code"><![CDATA[ 51 <command detect_errors="aggressive"><![CDATA[
52 #set compressed = 'no' 52 #set compressed = 'no'
53 #if $singlePaired.sPaired == "single": 53 #if $singlePaired.sPaired == "single":
54 #if $singlePaired.input_singles.is_of_type("fastq.gz"): 54 #if $singlePaired.input_singles.is_of_type("fastq.gz"):
55 #set read1 = 'input_1.fastq.gz' 55 #set read1 = 'input_1.fastq.gz'
56 #set compressed = 'gz' 56 #set compressed = 'gz'
130 $rrbs.rrbs 130 $rrbs.rrbs
131 $rrbs.non_directional 131 $rrbs.non_directional
132 #end if 132 #end if
133 133
134 --output_dir ./ 134 --output_dir ./
135 --suppress_warn
136 135
137 #if $params.settingsType == "custom" and not $params.report: 136 #if $params.settingsType == "custom" and not $params.report:
138 --no_report_file 137 --no_report_file
139 #end if 138 #end if
140 139
383 <param name="input_mate1" value="bwa-mem-fastq1.fq.gz" ftype="fastqsanger.gz" /> 382 <param name="input_mate1" value="bwa-mem-fastq1.fq.gz" ftype="fastqsanger.gz" />
384 <param name="input_mate2" value="bwa-mem-fastq2.fq.gz" ftype="fastqsanger.gz" /> 383 <param name="input_mate2" value="bwa-mem-fastq2.fq.gz" ftype="fastqsanger.gz" />
385 <param name="sPaired" value="paired" /> 384 <param name="sPaired" value="paired" />
386 <param name="settingsType" value="custom" /> 385 <param name="settingsType" value="custom" />
387 <param name="report" value="true" /> 386 <param name="report" value="true" />
388 <output name="trimmed_reads_pair1" file="paired_example_pair1_results2.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="0"/> 387 <output name="trimmed_reads_pair1" file="paired_example_pair1_results2.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="30"/>
389 <output name="trimmed_reads_pair2" file="paired_example_pair2_results2.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="0"/> 388 <output name="trimmed_reads_pair2" file="paired_example_pair2_results2.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="30"/>
390 <output name="report_file" file="paired_example_results2gz.txt" ftype="txt" lines_diff="24" /> 389 <output name="report_file" file="paired_example_results2gz.txt" ftype="txt" lines_diff="24" />
391 </test> 390 </test>
392 391
393 <test> 392 <test>
394 <param name="input_mate_pairs"> 393 <param name="input_mate_pairs">
429 <param name="retain_unpaired_select" value="retain_unpaired_output" /> 428 <param name="retain_unpaired_select" value="retain_unpaired_output" />
430 429
431 <output name="report_file" file="paired_collection_example_results3gz.txt" ftype="txt" lines_diff="25" /> 430 <output name="report_file" file="paired_collection_example_results3gz.txt" ftype="txt" lines_diff="25" />
432 431
433 <output_collection name="trimmed_reads_paired_collection" type="paired"> 432 <output_collection name="trimmed_reads_paired_collection" type="paired">
434 <element name="forward" file="paired_collection_example_pair1_results3.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="0"/> 433 <element name="forward" file="paired_collection_example_pair1_results3.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="30"/>
435 <element name="reverse" file="paired_collection_example_pair2_results3.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="0"/> 434 <element name="reverse" file="paired_collection_example_pair2_results3.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="30"/>
436 </output_collection> 435 </output_collection>
437 436
438 <output_collection name="trimmed_reads_unpaired_collection" type="paired"> 437 <output_collection name="trimmed_reads_unpaired_collection" type="paired">
439 <element name="forward" file="paired_collection_example_unpair1_results3.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="0"/> 438 <element name="forward" file="paired_collection_example_unpair1_results3.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="30"/>
440 <element name="reverse" file="paired_collection_example_unpair2_results3.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="0"/> 439 <element name="reverse" file="paired_collection_example_unpair2_results3.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="30"/>
441 </output_collection> 440 </output_collection>
442 </test> 441 </test>
443 </tests> 442 </tests>
444 <help><![CDATA[ 443 <help><![CDATA[
445 **What it does** 444 **What it does**