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comparison fastp.xml @ 12:d60c3f704da0 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6b8fbd9db12329e2f49eee672b185015c3e35d4f
author iuc
date Tue, 13 Aug 2024 12:18:39 +0000
parents c59d48774d03
children dbfc505896e9
comparison
equal deleted inserted replaced
11:c59d48774d03 12:d60c3f704da0
1 <tool id="fastp" name="fastp" version="@TOOL_VERSION@+galaxy0" profile="23.1"> 1 <tool id="fastp" name="fastp" version="@TOOL_VERSION@+galaxy1" profile="23.1">
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 <expand macro="biotools" /> 6 <expand macro="biotools" />
71 #end if 71 #end if
72 72
73 #if str($single_paired.single_paired_selector).startswith('paired'): 73 #if str($single_paired.single_paired_selector).startswith('paired'):
74 #if str($single_paired.adapter_trimming_options.adapter_sequence2): 74 #if str($single_paired.adapter_trimming_options.adapter_sequence2):
75 --adapter_sequence_r2 '$single_paired.adapter_trimming_options.adapter_sequence2' 75 --adapter_sequence_r2 '$single_paired.adapter_trimming_options.adapter_sequence2'
76 #else 76 #end if
77 --detect_adapter_for_pe 77 $single_paired.adapter_trimming_options.detect_adapter_for_pe
78 #end if
79 #end if 78 #end if
80 79
81 80
82 ## Global Trimming Options 81 ## Global Trimming Options
83 82
224 <when value="paired"> 223 <when value="paired">
225 <expand macro="in" read_number="1" argument="-i"/> 224 <expand macro="in" read_number="1" argument="-i"/>
226 <expand macro="in" read_number="2" argument="-I"/> 225 <expand macro="in" read_number="2" argument="-I"/>
227 <expand macro="adapter_trimming_options"> 226 <expand macro="adapter_trimming_options">
228 <expand macro="adapter_sequence" read_number="2"/> 227 <expand macro="adapter_sequence" read_number="2"/>
228 <expand macro="detect_adapter_for_pe" />
229 </expand> 229 </expand>
230 <expand macro="global_trimming_options_paired" /> 230 <expand macro="global_trimming_options_paired" />
231 </when> 231 </when>
232 <when value="paired_collection"> 232 <when value="paired_collection">
233 <param name="paired_input" type="data_collection" format="fastq,fastq.gz" label="Select paired collection(s)" collection_type="paired"/> 233 <param name="paired_input" type="data_collection" format="fastq,fastq.gz" label="Select paired collection(s)" collection_type="paired"/>
234 <expand macro="adapter_trimming_options"> 234 <expand macro="adapter_trimming_options">
235 <expand macro="adapter_sequence" read_number="2"/> 235 <expand macro="adapter_sequence" read_number="2"/>
236 <expand macro="detect_adapter_for_pe" />
236 </expand> 237 </expand>
237 <expand macro="global_trimming_options_paired" /> 238 <expand macro="global_trimming_options_paired" />
238 </when> 239 </when>
239 </conditional> 240 </conditional>
240 241