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

"planemo upload commit 5d3fc4232e0e036ac1ed9e2c36adc41d6af4987f"

4:70cb5527defb

<tool id="umi_tools_count" name="UMI-tools count" version="@VERSION@.0">
    <description>performs quantification of UMIs from BAM files</description>
    <macros>
        <import>macros.xml</import>
        <xml name="sanitize_tag" >
            <sanitizer invalid_char="">

-\-gene-tag or -\-per-contig option" /> -->
            <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." >
                <expand macro="sanitize_tag" />
            </param>
            <param argument="--skip-tags-regex" name="skip_tags_regex" type="text" label="Skip any reads where the gene matches this tag" value="" >
                <sanitizer invalid_char="">
                    <valid initial="string.letters,string.digits">
                        <add value="!="/>
                        <add value="-"/>
                        <add value="_"/>
                        <add value="."/>
                        <add value="?"/>
                        <add value="&lt;"/><!-- left triangle bracket -->
                        <add value="&gt;"/><!-- right triangle bracket -->
                        <add value="&#91;"/> <!-- left square bracket -->
                        <add value="&#93;"/> <!-- right square bracket -->
                        <add value="&#94;"/> <!-- caret -->
                        <add value="&#123;"/> <!-- left curly -->
                        <add value="&#125;"/> <!-- right curly -->
                        <add value="&#40;"/> <!-- left parenthesis -->
                        <add value="&#41;"/> <!-- right parenthesis -->
                    </valid>
                </sanitizer>
            </param>
            <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." />
            <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." />
            <param argument="--random-seed" name="random_seed" type="integer" min="0" value="0" label="Random Seed" />
        </section>

5:933220bbc2ae

<tool id="umi_tools_count" name="UMI-tools count" version="@VERSION@.1">
    <description>performs quantification of UMIs from BAM files</description>
    <macros>
        <import>macros.xml</import>
        <xml name="sanitize_tag" >
            <sanitizer invalid_char="">

-\-gene-tag or -\-per-contig option" /> -->
            <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." >
                <expand macro="sanitize_tag" />
            </param>
            <param argument="--skip-tags-regex" name="skip_tags_regex" type="text" label="Skip any reads where the gene matches this tag" value="" >
                <expand macro="barcode_sanitizer" />
            </param>
            <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." />
            <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." />
            <param argument="--random-seed" name="random_seed" type="integer" min="0" value="0" label="Random Seed" />
        </section>