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comparison fastp.xml @ 6:a935cbdf1c0e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 72f3e06941d063dffce10741fcebea38a536ee15
author iuc
date Thu, 23 Aug 2018 02:53:34 -0400
parents 3e2551a37201
children 6c2351178f8d
comparison
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5:3e2551a37201 6:a935cbdf1c0e
1 <tool id="fastp" name="fastp" version="@WRAPPER_VERSION@.2"> 1 <tool id="fastp" name="fastp" version="@WRAPPER_VERSION@.3">
2 <description>- fast all-in-one preprocessing for FASTQ files</description> 2 <description>- fast all-in-one preprocessing for FASTQ files</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
152 152
153 ## PolyX tail trimming 153 ## PolyX tail trimming
154 154
155 #if $read_mod_options.polyx_tail_trimming.polyx_trimming_select == '-x': 155 #if $read_mod_options.polyx_tail_trimming.polyx_trimming_select == '-x':
156 $read_mod_options.polyx_tail_trimming.polyx_trimming_select 156 $read_mod_options.polyx_tail_trimming.polyx_trimming_select
157 #if str($read_mod_options.polyg_tail_trimming.poly_g_min_len): 157 #if str($read_mod_options.polyx_tail_trimming.poly_x_min_len):
158 --poly_x_min_len $read_mod_options.polyx_tail_trimming.poly_x_min_len 158 --poly_x_min_len $read_mod_options.polyx_tail_trimming.poly_x_min_len
159 #end if 159 #end if
160 #end if 160 #end if
161 161
162 ## UMI processing 162 ## UMI processing
258 </section> 258 </section>
259 259
260 <!-- Read Modification Options --> 260 <!-- Read Modification Options -->
261 <section name="read_mod_options" title="Read Modification Options"> 261 <section name="read_mod_options" title="Read Modification Options">
262 <conditional name="polyg_tail_trimming"> 262 <conditional name="polyg_tail_trimming">
263 <param name="trimming_select" type="select" label="PolyG tail trimming" help="Useful for NextSeq/NovaSeq data"> 263 <param name="trimming_select" type="select" label="PolyG tail trimming" help="This feature is enabled for NextSeq/NovaSeq data by default. NextSeq/NovaSeq data is detected by the machine ID in the FASTQ records.">
264 <option value="" selected="true">Automatic trimming for Illumina NextSeq/NovaSeq data</option> 264 <option value="" selected="true">Automatic trimming for Illumina NextSeq/NovaSeq data</option>
265 <option value="-g">Force polyG tail trimming</option> 265 <option value="-g">Force polyG tail trimming</option>
266 <option value="-G">Disable polyG tail trimming</option> 266 <option value="-G">Disable polyG tail trimming</option>
267 </param> 267 </param>
268 <when value="-g"> 268 <when value="-g">
442 <param name="single_paired_selector" value="single"/> 442 <param name="single_paired_selector" value="single"/>
443 <param name="trimming_select" value="-g"/> 443 <param name="trimming_select" value="-g"/>
444 <param name="poly_g_min_len" value="10"/> 444 <param name="poly_g_min_len" value="10"/>
445 <output name="out1" ftype="fastq.gz" decompress="True" file="out1.fq.gz"/> 445 <output name="out1" ftype="fastq.gz" decompress="True" file="out1.fq.gz"/>
446 </test> 446 </test>
447 <!-- Ensure polyX trimming works -->
448 <test expect_num_outputs="2">
449 <param name="in1" ftype="fastq.gz" value="R1.fq.gz"/>
450 <param name="single_paired_selector" value="single"/>
451 <param name="trimming_select" value="-G"/>
452 <param name="polyx_trimming_select" value="-x"/>
453 <param name="poly_x_min_len" value="10"/>
454 <output name="out1" ftype="fastq.gz" decompress="True" file="out1.fq.gz"/>
455 </test>
447 </tests> 456 </tests>
448 <help><![CDATA[ 457 <help><![CDATA[
449 .. class:: infomark 458 .. class:: infomark
450 459
451 **What it does** 460 **What it does**