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SVDetect_compare.xml |
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| diff -r ba8c5e544948 -r f6ccaaed3654 SVDetect_compare.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SVDetect_compare.xml Mon Jun 11 12:31:19 2012 -0400 |
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| @@ -0,0 +1,218 @@ +<tool id="svdetect_compare" name="Compare"> + +<description>structural variants between two samples</description> + +<command interpreter="perl">SVDetect_compare.pl links2compare -conf '$config_file' -l '$log_file' -N '$sample_name.$reference_name' + +#if $links2SV +-out1 '$common_sv_file' +-out2 '$sample_sv_file' +-out3 '$reference_sv_file' +#end if + +#if $file_conversion.file_conversion_select=="convert" and $file_conversion.links2circos +-out4 '$common_circos_file' +-out5 '$sample_circos_file' +-out6 '$reference_circos_file' +#end if + +#if $file_conversion.file_conversion_select=="convert" and $file_conversion.links2bed +-out7 '$common_bed_file' +-out8 '$sample_bed_file' +-out9 '$reference_bed_file' +#end if + +</command> + +<inputs> + <param name="sample_name" type="text" size="20" value="sample" label="Sample Name"/> + <param name="sample_read1_length" type="integer" size="10" value="50" label="Sample read 1 length (bp)"/> + <param name="sample_read2_length" type="integer" size="10" value="50" label="Sample read 2 length (bp)"/> + <param name="sample_mates_file" type="data" format="sv" label="Sample input file" help=".sv file"/> + + <param name="reference_name" type="text" size="20" value="reference" label="Reference Name"/> + <param name="reference_read1_length" type="integer" size="10" value="50" label="Reference read 1 length (bp)"/> + <param name="reference_read2_length" type="integer" size="10" value="50" label="Reference read 2 length (bp)"/> + <param name="reference_mates_file" type="data" format="sv" label="Reference input file" help=".sv file"/> + + <param name="min_overlap" type="float" size="10" value="0.05" label="Minimum overlap of links required as a fraction"/> + <param name="same_sv_type" label="Comparison of SVs with the same type only ?" type="boolean" truevalue="1" falsevalue="0" checked="True"/> + + <param name="links2SV" label="Do you want to have filtered links in a tabulated file format showing significant SVs?" type="boolean" truevalue="1" falsevalue="0" checked="True"/> + + <conditional name="file_conversion"> + <param name="file_conversion_select" type="select" label="Output file conversion" help="Converts filtered links to Circos/BED files format for graphical view of SVs"> + <option value="do_not_convert">No</option> + <option value="convert">Yes</option> + </param> + <when value="do_not_convert"> + <!-- do nothing here --> + </when> + <when value="convert"> + <param name="links2circos" label="Converts the link list to the Circos link format" type="boolean" truevalue="1" falsevalue="0" checked="True"/> + <param name="links2bed" label="Converts the link list to the UCSC BED format" type="boolean" truevalue="1" falsevalue="0" checked="False"/> + <param name="organism_id" type="text" size="10" value="hs" label="Organism ID"/> + <repeat name="color_code" title="Color-code" min="1" max="7"> + <param name="color" type="select" label="Color"> + <option value="grey">grey</option> + <option value="black">black</option> + <option value="blue">blue</option> + <option value="green">green</option> + <option value="purple">purple</option> + <option value="orange">orange</option> + <option value="red">red</option> + </param> + <param name="interval" type="text" value="1,3" label="Interval"/> + </repeat> + </when> + </conditional> +</inputs> + + + +<outputs> + <data format="sv" name="common_sv_file" label="common.compared.sv"> + <filter>links2SV is True</filter> + </data> + <data format="sv" name="sample_sv_file" label="${sample_name}.compared.sv"> + <filter>links2SV is True</filter> + </data> + <data format="sv" name="reference_sv_file" label="${reference_name}.compared.sv"> + <filter>links2SV is True</filter> + </data> + + <data format="segdup" name="common_circos_file" label="common.compared.segdup"> + <filter>( + file_conversion['file_conversion_select']=="convert" and + file_conversion['links2circos'] is True + ) + </filter> + </data> + <data format="segdup" name="sample_circos_file" label="${sample_name}.compared.segdup"> + <filter>( + file_conversion['file_conversion_select']=="convert" and + file_conversion['links2circos'] is True + ) + </filter> + </data> + <data format="segdup" name="reference_circos_file" label="${reference_name}.compared.segdup"> + <filter>( + file_conversion['file_conversion_select']=="convert" and + file_conversion['links2circos'] is True + ) + </filter> + </data> + + <data format="bed" name="common_bed_file" label="common.compared.bed"> + <filter>( + file_conversion['file_conversion_select']=="convert" and + file_conversion['links2bed'] is True + ) + </filter> + </data> + <data format="bed" name="sample_bed_file" label="${sample_name}.compared.bed"> + <filter>( + file_conversion['file_conversion_select']=="convert" and + file_conversion['links2bed'] is True + ) + </filter> + </data> + <data format="bed" name="reference_bed_file" label="${reference_name}.compared.bed"> + <filter>( + file_conversion['file_conversion_select']=="convert" and + file_conversion['links2bed'] is True + ) + </filter> + </data> + + <data format="txt" name="log_file" label="${sample_name}.${reference_name}.svdetect_compare.log"/> +</outputs> + + + +<configfiles> + <configfile name="config_file"> +<general> +output_dir=$__new_file_path__/svdetect +</general> + +#if $file_conversion.file_conversion_select == "convert" +#if $file_conversion.links2circos +<circos> +organism_id=${file_conversion.organism_id} +<colorcode> +#for $color_repeat in $file_conversion.color_code +${color_repeat.color}=${color_repeat.interval} +#end for +</colorcode> +</circos> +#end if +#if $file_conversion.links2bed +<bed> +<colorcode> +#for $color_repeat in $file_conversion.color_code +#if str($color_repeat.color)== "grey" +190,190,190=${color_repeat.interval} +#end if +#if str($color_repeat.color)== "black" +0,0,0=${color_repeat.interval} +#end if +#if str($color_repeat.color)== "blue" +0,0,255=${color_repeat.interval} +#end if +#if str($color_repeat.color)== "green" +0,255,0=${color_repeat.interval} +#end if +#if str($color_repeat.color)== "purple" +153,50,205=${color_repeat.interval} +#end if +#if str($color_repeat.color)== "orange" +255,140,0=${color_repeat.interval} +#end if +#if str($color_repeat.color)== "red" +255,0,0=${color_repeat.interval} +#end if +#end for +</colorcode> +</bed> +#end if +#end if + +<compare> +list_samples=${sample_name},${reference_name} +list_read_lengths=${sample_read1_length}-${sample_read2_length},${reference_read1_length}-${reference_read2_length} +sample_link_file=${sample_mates_file} +reference_link_file=${reference_mates_file} +min_overlap=${min_overlap} +same_sv_type=${same_sv_type} +sv_output=${links2SV} +#if $file_conversion.file_conversion_select == "convert" +circos_output=${$file_conversion.links2circos} +bed_output=${$file_conversion.links2bed} +#end if +</compare> + + </configfile> +</configfiles> + + <help> +**What it does** + +SVDetect - Version : 0.8 + +Comparison of clusters between two samples to get common or sample-specific SVs + +This program is designed to compare filtered links between two anomalously mapped mate-pair/paired-end datasets +and to identify common and sample-specific SVs (like the usual sample/reference design). +Overlaps between coordinates of clusters and types of SVs are used as parameters of comparison. + +Manual documentation available at the http://svdetect.sourceforge.net/Site/Manual.html + +----- + +.. class:: infomark + +Contact Bruno Zeitouni (bruno.zeitouni@curie.fr) for any questions or concerns about the Galaxy implementation of SVDetect. + </help> + +</tool> |