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comparison fastp.xml @ 7:2fcdbf78caf9 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 249269561e1d3a767371c154677e5dd59147f7d7
author iuc
date Wed, 16 Jan 2019 04:01:17 -0500
parents 7c49e331a737
children 1eb1895ab19c
comparison
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6:7c49e331a737 7:2fcdbf78caf9
1 <tool id="fastp" name="fastp" version="@WRAPPER_VERSION@.3"> 1 <tool id="fastp" name="fastp" version="@WRAPPER_VERSION@">
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>
70 #end if 70 #end if
71 71
72 #if str($single_paired.single_paired_selector).startswith('paired'): 72 #if str($single_paired.single_paired_selector).startswith('paired'):
73 #if str($single_paired.adapter_trimming_options.adapter_sequence2): 73 #if str($single_paired.adapter_trimming_options.adapter_sequence2):
74 --adapter_sequence_r2 '$single_paired.adapter_trimming_options.adapter_sequence2' 74 --adapter_sequence_r2 '$single_paired.adapter_trimming_options.adapter_sequence2'
75 #else
76 --detect_adapter_for_pe
75 #end if 77 #end if
76 #end if 78 #end if
77 79
78 80
79 ## Global Trimming Options 81 ## Global Trimming Options
340 <has_text text="fastp report"/> 342 <has_text text="fastp report"/>
341 </assert_contents> 343 </assert_contents>
342 </output> 344 </output>
343 </test> 345 </test>
344 <!-- Ensure paired collection works --> 346 <!-- Ensure paired collection works -->
345 <test expect_num_outputs="3"> 347 <test expect_num_outputs="4">
346 <param name="single_paired_selector" value="paired_collection"/> 348 <param name="single_paired_selector" value="paired_collection"/>
347 <param name="paired_input"> 349 <param name="paired_input">
348 <collection type="paired"> 350 <collection type="paired">
349 <element name="forward" value="bwa-mem-fastq1.fq" ftype="fastqsanger" /> 351 <element name="forward" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />
350 <element name="reverse" value="bwa-mem-fastq2.fq" ftype="fastqsanger" /> 352 <element name="reverse" value="bwa-mem-fastq2.fq" ftype="fastqsanger" />