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SVDetect_run_parallel.xml |
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| diff -r 861783bb65d2 -r f7a84d31bd83 SVDetect_run_parallel.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SVDetect_run_parallel.xml Mon Jun 11 12:30:38 2012 -0400 |
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| b'@@ -0,0 +1,324 @@\n+<tool id="svdetect_run_parallel" name="Detect clusters of anomalously mapped pairs">\n+\n+<description>and identify structural variants</description>\n+\n+<command interpreter="perl">SVDetect_run_parallel.pl\n+\n+#if $getLinks.linking == "linking"\n+linking\n+<!-- -out1 \'$links_file\' -->\n+#end if\n+#if $getFilteredLinks.filtering == "filtering"\n+filtering\n+<!--- out2 \'$flinks_file\' -->\n+#if str($getFilteredLinks.links2SV) == "create"\n+links2SV\n+-out3 \'$sv_file\'\n+#end if\n+#if $getFilteredLinks.file_conversion.file_conversion_select=="convert" and str($getFilteredLinks.file_conversion.links2circos) == "create"\n+links2circos\n+-out4 \'$circos_file\'\n+#end if\n+#if $getFilteredLinks.file_conversion.file_conversion_select=="convert" and str($getFilteredLinks.file_conversion.links2bed) == "create"\n+links2bed\n+-out5 \'$bed_file\'\n+#end if\n+#end if\n+-conf \'$config_file\'\n+-l \'$log_file\'\n+-N \'$sample_name\'\n+\n+</command>\n+\n+<inputs>\n+\t<param name="sample_name" type="text" value="sample" label="Sample Name"/>\n+\t<param name="mates_file" format="bam" type="data" label="Input BAM file (.ab.bam)"/>\n+ \t<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"/>\n+ \t<param name="mates_orientation" type="select" format="txt" label="Type of sequencing technology and libraries">\n+\t\t<option value="FR">Illumina paired-ends</option>\n+\t\t<option value="RF">Illumina mate-pairs</option>\n+\t\t<option value="FR">SOLiD paired-ends</option>\n+\t\t<option value="RR">SOLiD mate-pairs</option>\n+ \t</param>\n+\t<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)"/>\n+\t<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)"/>\n+\t<param name="sv_type" type="select" format="txt" label="Type of SV to detect">\n+\t\t<option value="all">all types of SVs</option>\n+\t\t<option value="intra">intrachromosomal SVs only</option>\n+\t\t<option value="inter">interchromosomal SVs only</option>\n+ \t</param>\n+ \t\n+ \t<conditional name="getLinks">\n+ \t\t<param name="linking" type="select" label="Linking procedure" help="Detection and isolation of links">\n+\t\t\t<option value="linking">Yes</option>\n+\t\t\t<option value="">No, already done</option>\n+ \t\t</param>\n+\t\t<when value="">\n+ \t\t\t<!-- do nothing here -->\n+ \t\t</when>\n+ \t\t<when value="linking">\n+\t\t\t<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"/>\n+ \t\t\t<param name="window_size" type="integer" size="20" value="3000" label="Window size (bp)" help="Equal to at least \xe2\x80\x9c2\xc2\xb5+2\xe2\x88\x9a2\xcf\x83"/>\n+\t\t\t<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"/>\n+ \t\t</when>\n+ \t</conditional>\n+\n+ \t<conditional name="getFilteredLinks">\n+\t \t<param name="filtering" type="select" label="Filtering procedure" help="Filtering of links according different parameters and thresholds">\n+\t\t\t<option value="filtering">Yes</option>\n+ <option value="">No</option>\n+\t \t</param>\n+\t\t<when value="">\n+\t \t\t<!-- do nothing here -->\n+\t \t</when>\n+\t \t<when value="filtering">\n+\t\t\t\n+\t\t\t<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"/>\n+\t\t\t<param name="chromosomes" type="text" size="20" label="List of chromosome names to keep or exclude"/>\n+\t\t\t<param name="nb_pairs_threshold" type="integer" size="20" value="5" label="Minimum number of pairs in a cluster"/>\n+\t\t\n+\t\t\t<conditional name="filter1">\n+\t \t\t\t<param name='..b'lt;general>\n+input_format = bam\n+sv_type = ${sv_type}\n+mates_orientation=${mates_orientation}\n+read1_length=${read1_length}\n+read2_length=${read2_length}\n+mates_file=${mates_file}\n+cmap_file=${cmap_file}\n+tmp_dir=$__new_file_path__/svdetect/tmp\n+output_dir=$__new_file_path__/svdetect\n+num_threads=8\n+</general> \n+\n+#if $getLinks.linking == "linking"\n+<detection>\n+#if str($getLinks.splitmate) == "split"\n+split_mate_file=1\n+#else\n+split_mate_file=0\n+#end if\n+window_size=${getLinks.window_size}\n+step_length=${getLinks.step_length}\n+</detection> \n+#end if\n+\n+#if $getFilteredLinks.filtering == "filtering"\n+<filtering>\n+#if str($getFilteredLinks.splitlink) == "split"\n+split_link_file=1\n+#else\n+split_link_file=0\n+#end if\n+#if str($getFilteredLinks.chromosomes) != ""\n+chromosomes=${getFilteredLinks.chromosomes}\n+#end if\n+nb_pairs_threshold=${getFilteredLinks.nb_pairs_threshold}\n+#if $getFilteredLinks.filter1.strand_filtering == "strand"\n+strand_filtering=1\n+final_score_threshold=${getFilteredLinks.filter1.final_score_threshold}\n+#if $getFilteredLinks.filter1.filter2.order_filtering == "order"\n+order_filtering=1\n+mu_length=${getFilteredLinks.filter1.filter2.mu_length}\n+sigma_length=${getFilteredLinks.filter1.filter2.sigma_length}\n+nb_pairs_order_threshold=${getFilteredLinks.filter1.filter2.nb_pairs_order_threshold}\n+#if $getFilteredLinks.filter1.filter2.filter3.insert_size_filtering == "insert"\n+insert_size_filtering=1\n+indel_sigma_threshold=${getFilteredLinks.filter1.filter2.filter3.indel_sigma_threshold}\n+dup_sigma_threshold=${getFilteredLinks.filter1.filter2.filter3.dup_sigma_threshold}\n+singleton_sigma_threshold=${getFilteredLinks.filter1.filter2.filter3.singleton_sigma_threshold}\n+#else\n+insert_size_filtering=0\n+#end if\n+#else\n+order_filtering=0\n+#end if\n+#else\n+strand_filtering=0\n+#end if\n+</filtering> \n+#end if\n+\n+#if $getFilteredLinks.filtering == "filtering"\n+#if $getFilteredLinks.file_conversion.file_conversion_select == "convert"\n+#if str($getFilteredLinks.file_conversion.links2circos) == "create"\n+<circos>\n+organism_id=${getFilteredLinks.file_conversion.organism_id}\n+<colorcode>\n+#for $color_repeat in $getFilteredLinks.file_conversion.color_code\n+${color_repeat.color}=${color_repeat.interval}\n+#end for\n+</colorcode>\n+</circos>\n+#end if\n+#if str($getFilteredLinks.file_conversion.links2bed) == "create"\n+<bed>\n+<colorcode>\n+#for $color_repeat in $getFilteredLinks.file_conversion.color_code\n+#if str($color_repeat.color)== "grey"\n+190,190,190=${color_repeat.interval}\n+#end if\n+#if str($color_repeat.color)== "black"\n+0,0,0=${color_repeat.interval}\n+#end if\n+#if str($color_repeat.color)== "blue"\n+0,0,255=${color_repeat.interval}\n+#end if\n+#if str($color_repeat.color)== "green"\n+0,255,0=${color_repeat.interval}\n+#end if\n+#if str($color_repeat.color)== "purple"\n+153,50,205=${color_repeat.interval}\n+#end if\n+#if str($color_repeat.color)== "orange"\n+255,140,0=${color_repeat.interval}\n+#end if\n+#if str($color_repeat.color)== "red"\n+255,0,0=${color_repeat.interval}\n+#end if\n+#end for\n+</colorcode>\n+</bed>\n+#end if\n+#end if\n+#end if\t\n+\t</configfile>\n+</configfiles>\n+\n+ <help>\n+**What it does**\n+\n+SVDetect - Version : 0.8\n+\n+Parallel version (nCPU=8)\n+\n+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\n+\n+This tool aims to identifying structural variations (SVs) with both clustering and sliding-window strategies, and helping in their visualization at the genome scale.\n+SVDetect is compatible with SOLiD and Illumina (>=1.3) reads.\n+\n+Manual documentation available at the http://svdetect.sourceforge.net/Site/Manual.html\n+\n+-----\n+\n+.. class:: infomark\n+\n+Contact Bruno Zeitouni (bruno.zeitouni@curie.fr) for any questions or concerns about the Galaxy implementation of SVDetect.\n+\n+ </help>\n+\n+</tool>\n' |