Mercurial > repos > iuc > umi_tools_extract

comparison umi-tools_extract.xml @ 19:7a7e33d28f62 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bc1b362f6783d3fc0ed0f42c14687001d7ff5f7a
author iuc
date Sat, 05 Oct 2024 13:07:19 +0000
parents 7accf7407811
children
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18:015cf18f4a15 19:7a7e33d28f62
1 <tool id="umi_tools_extract" name="UMI-tools extract" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> 1 <tool id="umi_tools_extract" name="UMI-tools extract" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>Extract UMI from fastq files</description> 2 <description>Extract UMI from fastq files</description>
3 <expand macro="bio_tools"/>
4 <macros> 3 <macros>
5 <import>macros.xml</import> 4 <import>macros.xml</import>
6 </macros> 5 </macros>
6 <expand macro="bio_tools"/>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 @COMMAND_LINK@ 9 @COMMAND_LINK@
10 10
11 umi_tools extract 11 umi_tools extract
109 </when> 109 </when>
110 </conditional> 110 </conditional>
111 <expand macro="log_input_macro"/> 111 <expand macro="log_input_macro"/>
112 </inputs> 112 </inputs>
113 <outputs> 113 <outputs>
114 <data name="out" format_source="input_read1" label="${tool.name} on ${on_string}: Reads" > 114 <data name="out" format_source="input_read1" label="${tool.name} on ${on_string}: Forward reads" >
115 <filter>input_type_cond['input_type'] in ['single', 'paired']</filter> 115 <filter>input_type_cond['input_type'] in ['single', 'paired']</filter>
116 </data> 116 </data>
117 <data name="out2" format_source="input_read2" label="${tool.name} on ${on_string}: Reads2" > 117 <data name="out2" format_source="input_read2" label="${tool.name} on ${on_string}: Reverse reads" >
118 <filter>input_type_cond['input_type'] == 'paired'</filter> 118 <filter>input_type_cond['input_type'] == 'paired'</filter>
119 </data> 119 </data>
120 <collection name="out_paired_collection" type="paired" label="${tool.name} on ${on_string}: Reads"> 120 <collection name="out_paired_collection" type="paired" label="${tool.name} on ${on_string}: Reads">
121 <data name="forward" format_source="input_readpair" /> 121 <data name="forward" format_source="input_readpair" />
122 <data name="reverse" format_source="input_readpair" /> 122 <data name="reverse" format_source="input_readpair" />
134 <conditional name="extract_method_cond"> 134 <conditional name="extract_method_cond">
135 <param name="prime3" value="true" /> 135 <param name="prime3" value="true" />
136 </conditional> 136 </conditional>
137 <param name="quality_selector" value="true" /> 137 <param name="quality_selector" value="true" />
138 <param name="quality_filter_threshold" value="10" /> 138 <param name="quality_filter_threshold" value="10" />
139 <param name="quality_encoding" value="phred33" />
140 <param name="log" value="true"/> 139 <param name="log" value="true"/>
141 <output name="out" file="out_SE.fastq" ftype="fastqsanger" /> 140 <output name="out" file="out_SE.fastq" ftype="fastqsanger" />
142 <output name="out_log" > 141 <output name="out_log" >
143 <assert_contents> 142 <assert_contents>
144 <has_text text="Input Reads: 100" /> 143 <has_text text="Input Reads: 100" />