Mercurial > repos > plus91-technologies-pvt-ltd > softsearch

changeset 5:668b848e19ad draft

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author plus91-technologies-pvt-ltd
date Thu, 29 May 2014 07:40:05 -0400
parents 1ee772504223
children d1279d7ee007
files all_fasta.loc.sample fasta_indexes.loc softsearch.xml tool_data_table_conf.xml.sample
diffstat 4 files changed, 0 insertions(+), 185 deletions(-) [+]
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--- a/all_fasta.loc.sample	Thu May 29 07:35:53 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,18 +0,0 @@
-#This file lists the locations and dbkeys of all the fasta files
-#under the "genome" directory (a directory that contains a directory
-#for each build). The script extract_fasta.py will generate the file
-#all_fasta.loc. This file has the format (white space characters are
-#TAB characters):
-#
-#<unique_build_id>	<dbkey>		<display_name>	<file_path>
-#
-#So, all_fasta.loc could look something like this:
-#
-#apiMel3	apiMel3	Honeybee (Apis mellifera): apiMel3		/path/to/genome/apiMel3/apiMel3.fa
-#hg19canon	hg19		Human (Homo sapiens): hg19 Canonical		/path/to/genome/hg19/hg19canon.fa
-#hg19full	hg19		Human (Homo sapiens): hg19 Full			/path/to/genome/hg19/hg19full.fa
-#
-#Your all_fasta.loc file should contain an entry for each individual
-#fasta file. So there will be multiple fasta files for each build,
-#such as with hg19 above.
-#
--- a/fasta_indexes.loc	Thu May 29 07:35:53 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,32 +0,0 @@
-#This is a sample file distributed with Galaxy that enables tools
-#to use a directory of Samtools indexed sequences data files.  You will need
-#to create these data files and then create a fasta_indexes.loc file
-#similar to this one (store it in this directory) that points to
-#the directories in which those files are stored. The fasta_indexes.loc
-#file has this format (white space characters are TAB characters):
-#
-# <unique_build_id>	<dbkey>	<display_name>	<file_base_path>
-#
-#So, for example, if you had hg19 Canonical indexed stored in
-#
-# /depot/data2/galaxy/hg19/sam/,
-#
-#then the fasta_indexes.loc entry would look like this:
-#
-#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/depot/data2/galaxy/hg19/sam/hg19canon.fa
-#
-#and your /depot/data2/galaxy/hg19/sam/ directory
-#would contain hg19canon.fa and hg19canon.fa.fai files.
-#
-#Your fasta_indexes.loc file should include an entry per line for
-#each index set you have stored.  The file in the path does actually
-#exist, but it should never be directly used. Instead, the name serves
-#as a prefix for the index file.  For example:
-#
-#hg18canon	hg18	Human (Homo sapiens): hg18 Canonical	/depot/data2/galaxy/hg18/sam/hg18canon.fa
-#hg18full	hg18	Human (Homo sapiens): hg18 Full	/depot/data2/galaxy/hg18/sam/hg18full.fa
-#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/depot/data2/galaxy/hg19/sam/hg19canon.fa
-#hg19full	hg19	Human (Homo sapiens): hg19 Full	/depot/data2/galaxy/hg19/sam/hg19full.fa
-
-hg19	hg19	Test(fasta)	/home/plus91/galaxy-dist/data/chr1.small.fa
-hg19	hg19	hg19.fa	/home/plus91/archer_1.0.0/chromFa/hg19.fa
--- a/softsearch.xml	Thu May 29 07:35:53 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,53 +0,0 @@
-<?xml version="1.0"?>
-<tool id="SoftSearch" name="SoftSearch">
-  <description>for structure variation</description>
-  <command> #if $source.index_source=="history" 
-	        samtools index $bam_file ; samtools faidx $source.history_fasta_file ; $inc | ~/2.4/src/SoftSearch.pl -l $min_length_soft_clip -q $min_map_quality -r $min_depth_soft_clip_loc -m $min_no_discordant_read -s $no_sd_consider_discordant -b $bam_file -f $source.history_fasta_file -o $out_file1
-	    #else
-		samtools index $bam_file ; samtools faidx $source.ref_fasta.fields.path ; $inc | ~/2.4/src/SoftSearch.pl -l $min_length_soft_clip -q $min_map_quality -r $min_depth_soft_clip_loc -m $min_no_discordant_read -s $no_sd_consider_discordant -b $bam_file -f $source.ref_fasta.fields.path -o $out_file1
-	    #end if		
- </command>
-  <inputs>
-      <param name="bam_file" type="data"   format="bam" label="BAM Files" />
-	 <conditional name="source">
-            <param name="index_source" type="select" label="Choose the source for the reference list">
-                <option value="cached">Locally cached</option>
-                <option value="history">History</option>
-            </param>
-            <when value="history">
-                <param format="fasta" name="history_fasta_file" type="data" label="Fasta file from history."/>
-            </when>
-            <when value="cached">
-                  <param name="ref_fasta" type="select" >
-                    <options from_data_table="fasta_indexes">
-                    <validator type="no_options" message="No Fasta file is available" />
-                    </options>
-                  </param>
-            </when>
-        </conditional>
-      <param name="inc" type="hidden" value="n=$RANDOM" />
-     	<param name="min_length_soft_clip" type="integer" value="10" label="-l Minimum length of soft-clipped segment [5]" /> 
-        <param name="min_map_quality" type="integer" value="20" label="-q Minimum mapping quality [20]" /> 	
-	<param name="min_depth_soft_clip_loc" type="integer" value="10" label="-r Minimum depth of soft-clipped reads at position [5]" /> 
-	<param name="min_no_discordant_read" type="integer" value="10" label="-m Minimum number of discordant read pairs [5]" /> 
-	<param name="no_sd_consider_discordant" type="integer" value="4" label="-s Number of sd away from mean to be considered discordant" />       
-  </inputs>
-  <outputs>
-      <data format="vcf" name="out_file1" />
-  </outputs>
-  <help>
-  </help>
-</tool>
-
-
-
-
-
-
-
-
-
-
-
-
-
--- a/tool_data_table_conf.xml.sample	Thu May 29 07:35:53 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,82 +0,0 @@
-<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc-->
-<tables>
-    <!-- Locations of all fasta files under genome directory -->
-    <table name="all_fasta" comment_char="#">
-        <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/all_fasta.loc" />
-    </table>
-    <!-- Locations of indexes in the BFAST mapper format -->
-    <table name="bfast_indexes" comment_char="#">
-        <columns>value, dbkey, formats, name, path</columns>
-        <file path="tool-data/bfast_indexes.loc" />
-    </table>
-    <!-- Locations of nucleotide (mega)blast databases -->
-    <table name="blastdb" comment_char="#">
-        <columns>value, name, path</columns>
-        <file path="tool-data/blastdb.loc" />
-    </table>
-    <!-- Locations of protein (mega)blast databases -->
-    <table name="blastdb_p" comment_char="#">
-        <columns>value, name, path</columns>
-        <file path="tool-data/blastdb_p.loc" />
-    </table>
-    <!-- Locations of indexes in the BWA mapper format -->
-    <table name="bwa_indexes" comment_char="#">
-        <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/bwa_index.loc" />
-    </table>
-    <!-- Locations of indexes in the BWA color-space mapper format -->
-    <table name="bwa_indexes_color" comment_char="#">
-        <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/bwa_index_color.loc" />
-    </table>
-    <!-- Locations of MAF files that have been indexed with bx-python -->
-    <table name="indexed_maf_files">
-        <columns>name, value, dbkey, species</columns>
-        <file path="tool-data/maf_index.loc" />
-    </table>
-    <!-- Locations of fasta files appropriate for NGS simulation -->
-    <table name="ngs_sim_fasta" comment_char="#">
-        <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/ngs_sim_fasta.loc" />
-    </table>
-    <!-- Locations of PerM base index files -->
-    <table name="perm_base_indexes" comment_char="#">
-        <columns>value, name, path</columns>
-        <file path="tool-data/perm_base_index.loc" />
-    </table>
-    <!-- Locations of PerM color-space index files -->
-    <table name="perm_color_indexes" comment_char="#">
-        <columns>value, name, path</columns>
-        <file path="tool-data/perm_color_index.loc" />
-    </table>
-    <!-- Location of Picard dict file and other files -->
-    <table name="picard_indexes" comment_char="#">
-        <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/picard_index.loc" />
-    </table>
-    <!-- Location of Picard dict files valid for GATK -->
-    <table name="gatk_picard_indexes" comment_char="#">
-        <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/gatk_sorted_picard_index.loc" />
-    </table>
-    <!-- Available of GATK references -->
-    <table name="gatk_annotations" comment_char="#">
-        <columns>value, name, gatk_value, tools_valid_for</columns>
-        <file path="tool-data/gatk_annotations.txt" />
-    </table>
-    <!-- Location of SRMA dict file and other files -->
-    <table name="srma_indexes" comment_char="#">
-        <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/picard_index.loc" />
-    </table>
-    <!-- Location of Mosaik files -->
-    <table name="mosaik_indexes" comment_char="#">
-        <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/mosaik_index.loc" />
-    </table>
-    <table name="fasta_indexes" comment_char="#">
-        <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/fasta_indexes.loc" />
-    </table>
-</tables>