Mercurial > repos > iuc > umi_tools_count

comparison umi-tools_counts.xml @ 5:933220bbc2ae draft

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"planemo upload commit 5d3fc4232e0e036ac1ed9e2c36adc41d6af4987f"
author iuc
date Tue, 10 Sep 2019 14:28:47 -0400
parents 70cb5527defb
children 276b4111b253
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4:70cb5527defb 5:933220bbc2ae
1 <tool id="umi_tools_count" name="UMI-tools count" version="@VERSION@.0"> 1 <tool id="umi_tools_count" name="UMI-tools count" version="@VERSION@.1">
2 <description>performs quantification of UMIs from BAM files</description> 2 <description>performs quantification of UMIs from BAM files</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 <xml name="sanitize_tag" > 5 <xml name="sanitize_tag" >
6 <sanitizer invalid_char=""> 6 <sanitizer invalid_char="">
100 -\-gene-tag or -\-per-contig option" /> --> 100 -\-gene-tag or -\-per-contig option" /> -->
101 <param argument="--gene-tag" name="gene_tag" type="text" label="Deduplicate per gene." value="XT" help="The gene information is encoded in the bam read tag." > 101 <param argument="--gene-tag" name="gene_tag" type="text" label="Deduplicate per gene." value="XT" help="The gene information is encoded in the bam read tag." >
102 <expand macro="sanitize_tag" /> 102 <expand macro="sanitize_tag" />
103 </param> 103 </param>
104 <param argument="--skip-tags-regex" name="skip_tags_regex" type="text" label="Skip any reads where the gene matches this tag" value="" > 104 <param argument="--skip-tags-regex" name="skip_tags_regex" type="text" label="Skip any reads where the gene matches this tag" value="" >
105 <sanitizer invalid_char=""> 105 <expand macro="barcode_sanitizer" />
106 <valid initial="string.letters,string.digits">
107 <add value="!="/>
108 <add value="-"/>
109 <add value="_"/>
110 <add value="."/>
111 <add value="?"/>
112 <add value="&lt;"/><!-- left triangle bracket -->
113 <add value="&gt;"/><!-- right triangle bracket -->
114 <add value="&#91;"/> <!-- left square bracket -->
115 <add value="&#93;"/> <!-- right square bracket -->
116 <add value="&#94;"/> <!-- caret -->
117 <add value="&#123;"/> <!-- left curly -->
118 <add value="&#125;"/> <!-- right curly -->
119 <add value="&#40;"/> <!-- left parenthesis -->
120 <add value="&#41;"/> <!-- right parenthesis -->
121 </valid>
122 </sanitizer>
123 </param> 106 </param>
124 <param argument="--per-contig" name="per_contig" type="boolean" truevalue="--per-contig" falsevalue="" checked="false" label="Deduplicate per contig (field 3 in BAM; RNAME)" help="All reads with the same contig will be considered to have the same alignment position. This is useful if you have aligned to a reference transcriptome with one transcript per gene." /> 107 <param argument="--per-contig" name="per_contig" type="boolean" truevalue="--per-contig" falsevalue="" checked="false" label="Deduplicate per contig (field 3 in BAM; RNAME)" help="All reads with the same contig will be considered to have the same alignment position. This is useful if you have aligned to a reference transcriptome with one transcript per gene." />
125 <param argument="--per-cell" name="per_cell" type="boolean" truevalue="--per-cell" falsevalue="" checked="true" label="Group reads only if they have the same cell barcode." /> 108 <param argument="--per-cell" name="per_cell" type="boolean" truevalue="--per-cell" falsevalue="" checked="true" label="Group reads only if they have the same cell barcode." />
126 <param argument="--random-seed" name="random_seed" type="integer" min="0" value="0" label="Random Seed" /> 109 <param argument="--random-seed" name="random_seed" type="integer" min="0" value="0" label="Random Seed" />
127 </section> 110 </section>