Mercurial > repos > bzeitouni > svdetect
diff svdetect/SVDetect_run_parallel.xml @ 28:091714bd75a0 draft default tip
new release r0.8b
| author | bzeitouni |
|---|---|
| date | Tue, 22 Jan 2013 06:20:22 -0500 |
| parents | c284618dd8da |
| children |
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--- a/svdetect/SVDetect_run_parallel.xml Tue Nov 06 10:06:26 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,324 +0,0 @@ -<tool id="svdetect_run_parallel" name="Detect clusters of anomalously mapped pairs"> - -<description>and identify structural variants</description> - -<command interpreter="perl">SVDetect_run_parallel.pl - -#if $getLinks.linking == "linking" -linking -<!-- -out1 '$links_file' --> -#end if -#if $getFilteredLinks.filtering == "filtering" -filtering -<!--- out2 '$flinks_file' --> -#if str($getFilteredLinks.links2SV) == "create" -links2SV --out3 '$sv_file' -#end if -#if $getFilteredLinks.file_conversion.file_conversion_select=="convert" and str($getFilteredLinks.file_conversion.links2circos) == "create" -links2circos --out4 '$circos_file' -#end if -#if $getFilteredLinks.file_conversion.file_conversion_select=="convert" and str($getFilteredLinks.file_conversion.links2bed) == "create" -links2bed --out5 '$bed_file' -#end if -#end if --conf '$config_file' --l '$log_file' --N '$sample_name' - -</command> - -<inputs> - <param name="sample_name" type="text" value="sample" label="Sample Name"/> - <param name="mates_file" format="bam" type="data" label="Input BAM file (.ab.bam)"/> - <param name="cmap_file" format="len" type="data" label="Chromosomes list file (.len)" help="Tabulated file format with Chromosome ID (integer from 1), name and length"/> - <param name="mates_orientation" type="select" format="txt" label="Type of sequencing technology and libraries"> - <option value="FR">Illumina paired-ends</option> - <option value="RF">Illumina mate-pairs</option> - <option value="FR">SOLiD paired-ends</option> - <option value="RR">SOLiD mate-pairs</option> - </param> - <param name="read1_length" type="integer" size="10" value="50" label="Read 1 length (bp)" help="Length of the first read in a pair (left read)"/> - <param name="read2_length" type="integer" size="10" value="50" label="Read 2 length (bp)" help="Length of the second read in a pair (right read)"/> - <param name="sv_type" type="select" format="txt" label="Type of SV to detect"> - <option value="all">all types of SVs</option> - <option value="intra">intrachromosomal SVs only</option> - <option value="inter">interchromosomal SVs only</option> - </param> - - <conditional name="getLinks"> - <param name="linking" type="select" label="Linking procedure" help="Detection and isolation of links"> - <option value="linking">Yes</option> - <option value="">No, already done</option> - </param> - <when value=""> - <!-- do nothing here --> - </when> - <when value="linking"> - <param name="splitmate" label="Do you want to split the original mate file per chromosome for parallel computing?" type="boolean" truevalue="split" falsevalue="do_not_split" checked="True" help="Untick it if already done"/> - <param name="window_size" type="integer" size="20" value="3000" label="Window size (bp)" help="Equal to at least “2µ+2√2σ"/> - <param name="step_length" type="integer" size="20" value="250" label="Step length size (bp)" help="Equal to 1/2 or 1/4 of the window size"/> - </when> - </conditional> - - <conditional name="getFilteredLinks"> - <param name="filtering" type="select" label="Filtering procedure" help="Filtering of links according different parameters and thresholds"> - <option value="filtering">Yes</option> - <option value="">No</option> - </param> - <when value=""> - <!-- do nothing here --> - </when> - <when value="filtering"> - - <param name="splitlink" label="Do you want to split the original link file per chromosome for parallel computing?" type="boolean" truevalue="split" falsevalue="do_not_split" checked="False" help="Untick it if (the linking is) already done"/> - <param name="chromosomes" type="text" size="20" label="List of chromosome names to keep or exclude"/> - <param name="nb_pairs_threshold" type="integer" size="20" value="5" label="Minimum number of pairs in a cluster"/> - - <conditional name="filter1"> - <param name="strand_filtering" type="select" label="Strand filtering procedure"> - <option value="strand">Yes</option> - <option value="">No</option> - </param> - <when value=""> - <!-- do nothing here --> - </when> - <when value="strand"> - - <conditional name="filter2"> - <param name="order_filtering" type="select" label="Order filtering procedure"> - <option value="order">Yes</option> - <option value="">No</option> - </param> - <when value=""> - <!-- do nothing here --> - </when> - <when value="order"> - - <conditional name="filter3"> - <param name="insert_size_filtering" type="select" label="Insert-size filtering procedure"> - <option value="insert">Yes</option> - <option value="">No</option> - </param> - <when value=""> - <!-- do nothing here --> - </when> - <when value="insert"> - <param name="indel_sigma_threshold" type="float" size="20" value="3" label="Minimal number of sigma fold for the insert size filtering and to call insertions and deletions"/> - <param name="dup_sigma_threshold" type="float" size="20" value="3" label="minimal number of sigma fold for the insert size filtering to call tandem duplications"/> - <param name="singleton_sigma_threshold" type="float" size="20" value="4" label="Minimal number of sigma fold for the insert size filtering to call singletons" help="for Illumina mate-pairs only"/> - </when> - </conditional> - - <param name="mu_length" type="integer" size="20" value="3000" label="Mean insert size value (µ) of normally mapped mate-pairs, in bp"/> - <param name="sigma_length" type="integer" size="20" value="250" label="Calculated sd value (σ) from the distribution of normally mapped mate-pairs, in bp"/> - <param name="nb_pairs_order_threshold" type="integer" size="20" value="2" label="Minimal number of pairs in a subgroup of paired-end reads for balanced events"/> - </when> - </conditional> - - <param name="final_score_threshold" type="float" size="20" value="1.0" label="Minimal final filtering score for calling SVs" help="A value of 1 means all the pairs in a cluster were consistent between each other after applying filters"/> - </when> - </conditional> - - <param name="links2SV" label="Do you want to have filtered links in a tabulated file format showing significant SVs?" type="boolean" truevalue="create" falsevalue="do_not_create" 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="create" falsevalue="do_not_create" checked="True"/> - <param name="links2bed" label="Converts the link list to the UCSC BED format" type="boolean" truevalue="create" falsevalue="do_not_create" 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> - </when> - </conditional> -</inputs> - - -<outputs> - <!--<data format="txt" name="links_file" label="svdetect.links"> - <filter>getLinks['linking']=="linking"</filter> - </data> - <data format="txt" name="flinks_file" label="svdetect.links.filtered"> - <filter>getFilteredLinks['filtering']=="filtering"</filter> - </data>--> - <data format="sv" name="sv_file" label="${sample_name}.sv"> - <filter>( - getFilteredLinks['filtering']=="filtering" and - getFilteredLinks['links2SV'] is True - ) - </filter> - </data> - <data format="segdup" name="circos_file" label="${sample_name}.segdup"> - <filter>( - getFilteredLinks['filtering']=="filtering" and - getFilteredLinks['file_conversion']['file_conversion_select']=="convert" and - getFilteredLinks['file_conversion']['links2circos'] is True - ) - </filter> - </data> - <data format="bed" name="bed_file" label="${sample_name}.bed"> - <filter>( - getFilteredLinks['filtering']=="filtering" and - getFilteredLinks['file_conversion']['file_conversion_select']=="convert" and - getFilteredLinks['file_conversion']['links2bed'] is True - ) - </filter> - </data> - <data format="txt" name="log_file" label="${sample_name}.svdetect_run.log"/> -</outputs> - - - -<configfiles> - <configfile name="config_file"> -<general> -input_format = bam -sv_type = ${sv_type} -mates_orientation=${mates_orientation} -read1_length=${read1_length} -read2_length=${read2_length} -mates_file=${mates_file} -cmap_file=${cmap_file} -tmp_dir=$__new_file_path__/svdetect/tmp -output_dir=$__new_file_path__/svdetect -num_threads=8 -</general> - -#if $getLinks.linking == "linking" -<detection> -#if str($getLinks.splitmate) == "split" -split_mate_file=1 -#else -split_mate_file=0 -#end if -window_size=${getLinks.window_size} -step_length=${getLinks.step_length} -</detection> -#end if - -#if $getFilteredLinks.filtering == "filtering" -<filtering> -#if str($getFilteredLinks.splitlink) == "split" -split_link_file=1 -#else -split_link_file=0 -#end if -#if str($getFilteredLinks.chromosomes) != "" -chromosomes=${getFilteredLinks.chromosomes} -#end if -nb_pairs_threshold=${getFilteredLinks.nb_pairs_threshold} -#if $getFilteredLinks.filter1.strand_filtering == "strand" -strand_filtering=1 -final_score_threshold=${getFilteredLinks.filter1.final_score_threshold} -#if $getFilteredLinks.filter1.filter2.order_filtering == "order" -order_filtering=1 -mu_length=${getFilteredLinks.filter1.filter2.mu_length} -sigma_length=${getFilteredLinks.filter1.filter2.sigma_length} -nb_pairs_order_threshold=${getFilteredLinks.filter1.filter2.nb_pairs_order_threshold} -#if $getFilteredLinks.filter1.filter2.filter3.insert_size_filtering == "insert" -insert_size_filtering=1 -indel_sigma_threshold=${getFilteredLinks.filter1.filter2.filter3.indel_sigma_threshold} -dup_sigma_threshold=${getFilteredLinks.filter1.filter2.filter3.dup_sigma_threshold} -singleton_sigma_threshold=${getFilteredLinks.filter1.filter2.filter3.singleton_sigma_threshold} -#else -insert_size_filtering=0 -#end if -#else -order_filtering=0 -#end if -#else -strand_filtering=0 -#end if -</filtering> -#end if - -#if $getFilteredLinks.filtering == "filtering" -#if $getFilteredLinks.file_conversion.file_conversion_select == "convert" -#if str($getFilteredLinks.file_conversion.links2circos) == "create" -<circos> -organism_id=${getFilteredLinks.file_conversion.organism_id} -<colorcode> -#for $color_repeat in $getFilteredLinks.file_conversion.color_code -${color_repeat.color}=${color_repeat.interval} -#end for -</colorcode> -</circos> -#end if -#if str($getFilteredLinks.file_conversion.links2bed) == "create" -<bed> -<colorcode> -#for $color_repeat in $getFilteredLinks.file_conversion.color_code -#if str($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 -#end if - </configfile> -</configfiles> - - <help> -**What it does** - -SVDetect - Version : 0.8 - -Parallel version (nCPU=8) - -SVDetect is a application for the isolation and the type prediction of intra- and inter-chromosomal rearrangements from paired-end/mate-pair sequencing data provided by the high-throughput sequencing technologies - -This tool aims to identifying structural variations (SVs) with both clustering and sliding-window strategies, and helping in their visualization at the genome scale. -SVDetect is compatible with SOLiD and Illumina (>=1.3) reads. - -Manual documentation available at the http://svdetect.sourceforge.net/Site/Manual.html - ------ - -.. class:: infomark - -Contact Bruno Zeitouni (svdetect@curie.fr) for any questions or concerns about the Galaxy implementation of SVDetect. - - </help> - -</tool>