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changeset 12:602e6912ac67 draft

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Deleted selected files
author bzeitouni
date Mon, 11 Jun 2012 12:56:50 -0400
parents f910d27718be
children f090bf6ec765
files BAM_preprocessingPairs.xml SVDetect_import.sh SVDetect_import.xml
diffstat 3 files changed, 0 insertions(+), 177 deletions(-) [+]
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--- a/BAM_preprocessingPairs.xml	Mon Jun 11 12:55:48 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,77 +0,0 @@
-<tool id="svdetect_preprocessing" name="BAM preprocessing">
-
-  <description>to get abnormal pairs</description>
-
-  <command interpreter="perl"> BAM_preprocessingPairs.pl -t '$readType' -p '$pairType' -n '$nbrePair' -s '$isizeMin' -S '$isizeMax' -f '$foldPair' -o $__new_file_path__/svdetect -b '$abBAM' -l '$log' -N $sample_name
-	#if $newBam.pairNormal=="yes" 
-	-d -x '$normBAM'
-	#end if
-	'$inputBam'
-  </command>
-
-  <inputs>
-    <param name="sample_name" type="text" value="sample" label="Sample Name"/>
-    <param name="inputBam" type="data" format="bam" label="BAM input file"/>
-    <param name="readType" type="select" label="Read type">
-	<option value="1">Illumina</option>
-	<option value="0">SOLiD</option>
-   </param>
-   <param name="pairType" type="select" label="Library type">
-	<option value="1">Paired-end</option>
-	<option value="0">Mate-Pair</option>
-   </param>
-   <conditional name="newBam">
-   <param name="pairNormal" type="select" label="Do you want an additional bam file listing concordant mapped pairs?" help="Dump normal pairs into a file sample_name.norm.bam/sam">
-	<option value="no">No</option>
-	<option value="yes">Yes</option>
-   </param>
-    <when value="yes">
-	  <!-- do nothing here -->
-    </when>
-    <when value="no">
-	 <!-- do nothing here -->
-    </when>
-   </conditional>
-   <param name="nbrePair" value="1000000" type="integer" size="30" label="Number of pairs for calculating mu (µ) and sigma (σ) lengths"/>
-   <param name="isizeMin" value="0" type="integer" size="30" label="Minimum value of ISIZE for calculating mu (µ) and sigma (σ) lengths"/>
-   <param name="isizeMax" value="10000" type="integer" size="30" label="Maximum value of ISIZE for calculating mu (µ)and sigma( σ) lengths"/>
-   <param name="foldPair" value="3" type="float" size="30" label="Minimal number of sigma (σ) fold for filtering pairs"/>
-  </inputs>
-
-  <outputs>
-    <data format="bam" name="abBAM" label="${$sample_name}.ab.bam"/> 
-    <data format="txt" name="log" label="${$sample_name}.svdetect_preprocessing.log"/>
-    <data format="bam" name="normBAM" label="${$sample_name}.norm.bam">
-    <filter>newBam['pairNormal'] == 'yes'</filter>
-    </data> 
-  </outputs>
-
-  <help>
-
-**What it does**
-
-Bam_preprocessingPairs - Version 0.4b
-
-Preprocessing of mates to get anomalously mapped mate-pair/paired-end reads as input for SVDetect.
-
-From all pairs mapped onto the reference genome, this script outputs abnormal pairs:
-
-	* mapped on two different chromosomes
-	* with an incorrect strand orientation and/or pair order
-	* with an insert size distance +- sigma threshold
-
-into a file prefix.ab.bam/sam sorted by read names
-    
--BAM/SAM File input format only.
-  
-SAMtools required for BAM files
-
------
-
-.. class:: infomark
-
-Contact Bruno Zeitouni (bruno.zeitouni@curie.fr) for any questions or concerns about the Galaxy implementation of SVDetect.
-
-  </help>
-
-</tool>
--- a/SVDetect_import.sh	Mon Jun 11 12:55:48 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,15 +0,0 @@
-#!/bin/bash
-
-
-while getopts "i:o:" optionName; do
-case "$optionName" in
-
-i) INPUT="$OPTARG";;
-o) OUTPUT="$OPTARG";;
-
-esac
-done
-
-rm $OUTPUT
-
-ln -s $INPUT $OUTPUT
--- a/SVDetect_import.xml	Mon Jun 11 12:55:48 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,85 +0,0 @@
-<tool id="svdetect_import" name="Import data">
-  <description>BAM, chromosome info or sv files</description>
-  <command interpreter="bash">SVDetect_import.sh -i $file_path
-  #if str($type.file_type)=="bam"
-  -o $outbamfile
-  #elif str($type.file_type)=="len"
-  -o $outlenfile
-  #elif str($type.file_type)=="sv"
-  -o $outsvfile
-  #end if
-  </command>
-  <inputs>
-    <param name="file_name" type="text" value="file1" label="File Name"/>
-    <conditional name="type">
-      <param name="file_type" type="select" label="Select the file type to import" help="BAM file (BAM) or text file (SAM, chromosome list or a SV tabulated text file)">
-          <option value="bam">BAM file (.bam)</option>
-          <option value="len">Chromosome info file (.len)</option>
-          <option value="sv">SVDetect output file (.sv)</option>
-      </param>
-    <when value="bam">
-      <!-- do nothing here -->
-    </when>
-    <when value="len">
-      <!-- do nothing here -->
-    </when>
-     <when value="sv">
-      <!-- do nothing here -->
-    </when>
-    </conditional>
-     <param name="file_path" type="text" size="150" label="Path to file"/>
-  </inputs>
-  <outputs>
-    <data format="bam" name="outbamfile" label="${file_name}.bam">
-      <filter>type['file_type']=="bam"</filter>
-    </data>
-    <data format="len" name="outlenfile" label="${file_name}.len">
-      <filter>type['file_type']=="len"</filter>
-    </data>
-    <data format="sv" name="outsvfile" label="${file_name}.sv">
-      <filter>type['file_type']=="sv"</filter>
-    </data>
-  </outputs>
-  <help>
-**What it does**
-
-This tool allows you to import quickly a BAM file, a chromosome info file or a SVDetect output file from you computer as inputs for SVDetect.
-
-
-**Example of chromosome file**
-
-Input len file::
-
-    1  chr1  247249719
-    2  chr2  242951149
-    3  chr3  199501827
-    4  chr4  191273063
-    5  chr5  180857866
-    6  chr6  170899992
-    7  chr7  158821424
-    8  chr8  146274826
-    9  chr9  140273252
-    10  chr10  135374737
-    11  chr11  134452384
-    12  chr12  132349534
-    13  chr13  114142980
-    14  chr14  106368585
-    15  chr15  100338915
-    16  chr16  88827254
-    17  chr17  78774742
-    18  chr18  76117153
-    19  chr19  63811651
-    20  chr20  62435964
-    21  chr21  46944323
-    22  chr22  49691432
-    23  chrX  154913754
-    24  chrY  57772954
-
------
-
-.. class:: infomark
-
-Contact Bruno Zeitouni (bruno.zeitouni@curie.fr) for any questions or concerns about the Galaxy implementation of SVDetect.
-  </help>
-
-</tool>