Mercurial > repos > iuc > umi_tools_extract

comparison umi-tools_extract.xml @ 12:d5ff68d2d5ff draft

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"planemo upload commit 5d3fc4232e0e036ac1ed9e2c36adc41d6af4987f"
author iuc
date Tue, 10 Sep 2019 14:28:00 -0400
parents a472e995d157
children 9fa7803d1c51
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11:a472e995d157 12:d5ff68d2d5ff
1 <tool id="umi_tools_extract" name="UMI-tools extract" version="@VERSION@.0"> 1 <tool id="umi_tools_extract" name="UMI-tools extract" version="@VERSION@.1">
2 <description>Extract UMI from fastq files</description> 2 <description>Extract UMI from fastq files</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 <macro name="out_conditional"> 5 <macro name="out_conditional">
6 <actions> 6 <actions>
103 <param name="bc_pattern" argument="--bc-pattern" type="text" label="Barcode pattern for first read" 103 <param name="bc_pattern" argument="--bc-pattern" type="text" label="Barcode pattern for first read"
104 help="Use this option to specify the format of the UMI/barcode. Use Ns to 104 help="Use this option to specify the format of the UMI/barcode. Use Ns to
105 represent the random positions and Xs to indicate the bc positions. 105 represent the random positions and Xs to indicate the bc positions.
106 Bases with Ns will be extracted and added to the read name. Remaining 106 Bases with Ns will be extracted and added to the read name. Remaining
107 bases, marked with an X will be reattached to the read."> 107 bases, marked with an X will be reattached to the read.">
108 <sanitizer invalid_char=""> 108 <expand macro="barcode_sanitizer" />
109 <valid initial="string.letters,string.digits">
110 <add value="!="/>
111 <add value="-"/>
112 <add value="_"/>
113 <add value="."/>
114 <add value="?"/>
115 <add value="&lt;"/><!-- left triangle bracket -->
116 <add value="&gt;"/><!-- right triangle bracket -->
117 <add value="&#91;"/> <!-- left square bracket -->
118 <add value="&#93;"/> <!-- right square bracket -->
119 <add value="&#94;"/> <!-- caret -->
120 <add value="&#123;"/> <!-- left curly -->
121 <add value="&#125;"/> <!-- right curly -->
122 <add value="&#40;"/> <!-- left parenthesis -->
123 <add value="&#41;"/> <!-- right parenthesis -->
124 </valid>
125 </sanitizer>
126 </param> 109 </param>
127 110
128 <param name="prime3" argument="--3prime" type="boolean" label="Is the barcode at the 5' end?" 111 <param name="prime3" argument="--3prime" type="boolean" label="Is the barcode at the 5' end?"
129 truevalue="1" falsevalue="0" checked="true" 112 truevalue="1" falsevalue="0" checked="true"
130 help="By default the barcode is assumed to be on the 5' end of the read, but 113 help="By default the barcode is assumed to be on the 5' end of the read, but