Mercurial > repos > iuc > bedtools
diff genomeCoverageBed.xml @ 34:dde39ba9c031 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
| author | iuc |
|---|---|
| date | Mon, 29 Apr 2019 05:55:48 -0400 |
| parents | 4f7a5ccd2ae9 |
| children | 3e38c9b3214f |
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--- a/genomeCoverageBed.xml Mon Dec 17 14:23:31 2018 -0500 +++ b/genomeCoverageBed.xml Mon Apr 29 05:55:48 2019 -0400 @@ -1,41 +1,38 @@ -<tool id="bedtools_genomecoveragebed" name="bedtools Genome Coverage" version="@WRAPPER_VERSION@"> +<tool id="bedtools_genomecoveragebed" name="bedtools Genome Coverage" version="@TOOL_VERSION@"> <description>compute the coverage over an entire genome</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> <expand macro="stdio" /> - <command> -<![CDATA[ - bedtools genomecov - @GENOME_FILE_COVERAGE@ + <command><![CDATA[ +bedtools genomecov +@GENOME_FILE_COVERAGE@ + +$split +$strand - $split - $strand - - #if str($report.report_select) == "bg": - #if $report.zero_regions: - $report.zero_regions - #else: - -bg - #end if +#if str($report.report_select) == "bg": + #if $report.zero_regions: + $report.zero_regions + #else: + -bg + #end if - #if str($report.scale): - -scale $report.scale - #end if - #else: - #if str($report.max): - -max $report.max - #end if - #end if - $d - $dz - $five - $three - - > '$output' -]]> - </command> + #if str($report.scale): + -scale $report.scale + #end if +#else: + #if str($report.max): + -max $report.max + #end if +#end if +$d +$dz +$five +$three +> '$output' + ]]></command> <inputs> <conditional name="input_type"> <param name="input_type_select" type="select" label="Input type"> @@ -43,11 +40,11 @@ <option value="bam">BAM</option> </param> <when value="bed"> - <param format="@STD_BEDTOOLS_INPUTS@" name="input" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file" /> + <param name="input" argument="-i" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file" /> <expand macro="input_conditional_genome_file" /> </when> <when value="bam"> - <param format="bam" name="input" type="data" label="BAM file" /> + <param name="input" argument="-ibam" type="data" format="bam" label="BAM file" /> </when> </conditional> <conditional name="report"> @@ -56,35 +53,35 @@ <option value="hist">Data suiteable for Histogram</option> </param> <when value="bg"> - <param name="zero_regions" type="boolean" checked="False" truevalue="-bga" falsevalue="" - label="Report regions with zero coverage" help="If set, regions without any coverage will also be reported. (-bga)" /> - <param name="scale" type="float" value="1.0" + <param name="zero_regions" argument="-bga" type="boolean" truevalue="-bga" falsevalue="" checked="false" + label="Report regions with zero coverage" help="If set, regions without any coverage will also be reported" /> + <param argument="-scale" type="float" value="1.0" label="Scale the coverage by a constant factor" - help="Each bedGraph coverage value is multiplied by this factor before being reported. Useful for normalizing coverage by, e.g., reads per million (RPM). (-scale)" /> + help="Each bedGraph coverage value is multiplied by this factor before being reported. Useful for normalizing coverage by, e.g., reads per million (RPM)." /> </when> <when value="hist"> - <param name="max" type="integer" label="Specify max depth" value="0" - help="Combine all positions with a depth >= max into a single bin in the histogram. (-max)" /> + <param argument="-max" type="integer" value="0" label="Specify max depth" + help="Combine all positions with a depth >= max into a single bin in the histogram" /> </when> </conditional> <expand macro="split" /> - <param name="strand" type="select" label="Calculate coverage based on" help="(-strand)"> + <param argument="-strand" type="select" label="Calculate coverage based on"> <option value="">both strands combined</option> <option value="-strand +">positive strand only</option> <option value="-strand -">negative strand only</option> </param> - <param name="d" type="boolean" checked="False" truevalue="-d" falsevalue="" - label="Report the depth at each genome position with 1-based coordinates" help="(-d)" /> - <param name="dz" type="boolean" checked="False" truevalue="-dz" falsevalue="" - label="Report the depth at each genome position with 0-based coordinatess" help="(-dz)" /> - <param name="five" type="boolean" checked="False" truevalue="-5" falsevalue="" - label="Calculate coverage of 5’ positions" help="Instead of entire interval. (-5)" /> - <param name="three" type="boolean" checked="False" truevalue="-3" falsevalue="" - label="Calculate coverage of 3’ positions" help="Instead of entire interval. (-3)" /> + <param argument="-d" type="boolean" truevalue="-d" falsevalue="" checked="false" + label="Report the depth at each genome position with 1-based coordinates" /> + <param argument="-dz" type="boolean" truevalue="-dz" falsevalue="" checked="false" + label="Report the depth at each genome position with 0-based coordinatess" /> + <param name="five" argument="-5" type="boolean" truevalue="-5" falsevalue="" checked="false" + label="Calculate coverage of 5’ positions" help="Instead of entire interval" /> + <param name="three" argument="-3" type="boolean" truevalue="-3" falsevalue="" checked="false" + label="Calculate coverage of 3’ positions" help="Instead of entire interval" /> </inputs> <outputs> - <data format="bedgraph" name="output"> + <data name="output" format="bedgraph"> <change_format> <when input="report.report_select" value="hist" format="tabular" /> </change_format> @@ -100,8 +97,7 @@ <output name="output" file="genomeCoverageBed_result1.bed" ftype="tabular" /> </test> </tests> - <help> -<![CDATA[ + <help><![CDATA[ **What it does** This tool calculates the genome-wide coverage of intervals defined in a BAM or BED file and reports them in BedGraph format. @@ -168,7 +164,6 @@ @REFERENCES@ -]]> - </help> + ]]></help> <expand macro="citations" /> </tool>