| Previous changeset 4:70cb5527defb (2019-08-27) Next changeset 6:276b4111b253 (2019-12-05) |
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Commit message:
"planemo upload commit 5d3fc4232e0e036ac1ed9e2c36adc41d6af4987f" |
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modified:
macros.xml umi-tools_counts.xml |
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| diff -r 70cb5527defb -r 933220bbc2ae macros.xml --- a/macros.xml Tue Aug 27 17:11:32 2019 -0400 +++ b/macros.xml Tue Sep 10 14:28:47 2019 -0400 |
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| @@ -3,8 +3,6 @@ <macro name="barcode_sanitizer" > <sanitizer invalid_char=""> <valid initial="string.letters,string.digits"> - <add value="(" /><!-- left bracket --> - <add value=")" /><!-- right bracket --> <add value="*" /><!-- asterisk --> <add value="," /><!-- comma --> <add value="." /><!-- period --> @@ -13,8 +11,15 @@ <add value=">" /><!-- greater than --> <add value="?" /><!-- question mark --> <add value="_" /><!-- underscore --> + <add value="(" /><!-- left bracket --> + <add value=")" /><!-- right bracket --> + <add value="["/> <!-- left square bracket --> + <add value="]"/> <!-- right square bracket --> <add value="{"/><!-- left brace --> <add value="}"/><!-- right brace --> + <add value="^"/> <!-- caret --> + <add value="-"/> + <add value="!"/> </valid> </sanitizer> </macro> |
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| diff -r 70cb5527defb -r 933220bbc2ae umi-tools_counts.xml --- a/umi-tools_counts.xml Tue Aug 27 17:11:32 2019 -0400 +++ b/umi-tools_counts.xml Tue Sep 10 14:28:47 2019 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="umi_tools_count" name="UMI-tools count" version="@VERSION@.0"> +<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> @@ -102,24 +102,7 @@ <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="<"/><!-- left triangle bracket --> - <add value=">"/><!-- right triangle bracket --> - <add value="["/> <!-- left square bracket --> - <add value="]"/> <!-- right square bracket --> - <add value="^"/> <!-- caret --> - <add value="{"/> <!-- left curly --> - <add value="}"/> <!-- right curly --> - <add value="("/> <!-- left parenthesis --> - <add value=")"/> <!-- right parenthesis --> - </valid> - </sanitizer> + <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." /> |