changeset 100:bd86ab3d004c draft

Deleted selected files

--- a/fastq2sam_wrapper.sh	Mon Feb 24 17:27:59 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,15 +0,0 @@
-#!/bin/bash
-
-if [ "$1" == "sam" ]
-then
-    output=$2.sam
-else
-    output=$2
-fi
-
-java -XX:DefaultMaxRAMFraction=1 -XX:+UseParallelGC -jar "$JAVA_JAR_PATH/FastqToSam.jar" SAMPLE_NAME="$3" READ_GROUP_NAME="$4" OUTPUT=$output ${*:5}
-
-if [ "$1" == "sam" ]
-then
-    mv $2.sam $2
-fi

--- a/picard_FastqToSam.xml	Mon Feb 24 17:27:59 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,154 +0,0 @@
-<tool id="picard_FastqToSam" name="FASTQ to BAM / SAM" version="1.106.0">
-  <description>creates an unaligned BAM or SAM file</description>
-  <requirements><requirement type="package" version="1.106.0">picard</requirement></requirements>
-  <!-- Dan Blankenberg & dorine -->
-  
-  <command interpreter="bash">fastq2sam_wrapper.sh
-    "${outputtype}"
-    "${output_bam}"
-    "${sample_name}" 
-    "${read_group_name}"
-    FASTQ="${input_fastq1}"
-    #if str( $input_fastq2) != "None":
-        FASTQ2="${input_fastq2}"
-    #end if
-    QUALITY_FORMAT="${ dict( fastqsanger='Standard', fastqcssanger='Standard', fastqillumina='Illumina', fastqsolexa='Solexa' )[ $input_fastq1.ext ] }" ##Solexa, Illumina, Standard
-    #if $param_type.param_type_selector == "advanced":
-        #if str( $param_type.library_name ) != "":
-            LIBRARY_NAME="${param_type.library_name}" 
-        #end if
-        #if str( $param_type.platform_unit ) != "":
-            PLATFORM_UNIT="${param_type.platform_unit}"
-        #end if
-        #if str( $param_type.platform ) != "":
-            PLATFORM="${param_type.platform}"
-        #end if 
-        #if str( $param_type.sequencing_center ) != "":
-            SEQUENCING_CENTER="${param_type.sequencing_center}"
-        #end if 
-        #if str( $param_type.predicted_insert_size ) != "":
-            PREDICTED_INSERT_SIZE="${param_type.predicted_insert_size}"
-        #end if 
-        #if str( $param_type.description.value ) != "":
-            DESCRIPTION="${param_type.description}"
-        #end if 
-        #if str( $param_type.run_date ) != "":
-            RUN_DATE="${param_type.run_date}"
-        #end if
-        #if str( $param_type.min_q ) != "":
-            MIN_Q="${param_type.min_q}"
-        #end if
-        #if str( $param_type.max_q ) != "":
-            MAX_Q="${param_type.max_q}"
-        #end if
-        SORT_ORDER="${param_type.sort_order}"
-    #else:
-        SORT_ORDER=coordinate ##unsorted, queryname, coordinate; always use coordinate
-    #end if
-  2&gt;&amp;1 
-  || echo "Error running Picard FastqToSAM" >&amp;2
-  </command>
-  <inputs>
-    <param name="input_fastq1" type="data" format="fastqsanger,fastqcsanger,fastqillumina,fastqsolexa" label="FASTQ file" /> 
-    <param name="input_fastq2" type="data" format="fastqsanger,fastqcsanger,fastqillumina,fastqsolexa" optional="True" label="Second FASTQ of paired end data" help="Only needed when using paired end data." >
-      <options options_filter_attribute="ext" from_parameter="tool.app.datatypes_registry.datatypes_by_extension" transform_lines="obj.keys()">
-        <column name="name" index="0"/>
-        <column name="value" index="0"/>
-        <filter type="param_value" ref="input_fastq1" ref_attribute="ext" column="0"/> 
-      </options>
-    </param>
-    <param name="read_group_name" type="text" value="A" label="Read Group Name" />
-    <param name="sample_name" type="text" value="unknown_sample" label="Sample Name" />
-    <conditional name="param_type">
-      <param name="param_type_selector" type="select" label="Basic or Advanced options">
-        <option value="basic" selected="True">Basic</option>
-        <option value="advanced">Advanced</option>
-      </param>
-      <when value="basic">
-        <!-- Do nothing here -->
-      </when>
-      <when value="advanced">
-        <param name="library_name" type="text" value="" label="Library Name" />
-        <param name="platform_unit" type="text" value="" label="Platform Unit" />
-        <param name="platform" type="text" value="" label="Platform" />
-        <param name="sequencing_center" type="text" value="" label="Sequencing Center" />
-        <param name="predicted_insert_size" type="integer" value="" optional="True" label="Predicted Insert Size" />
-        <param name="description" type="text" value="" label="Description" />
-        <param name="run_date" type="text" value="" label="Run Date" />
-        <param name="min_q" type="integer" optional="True" value="0" label="Min Q" />
-        <param name="max_q" type="integer" optional="True" value="93" label="Max Q" />
-        <param name="sort_order" type="select" label="Sort order">
-          <option value="coordinate" selected="True">coordinate</option>
-          <option value="queryname">queryname</option>
-          <option value="unsorted">unsorted</option>
-        </param>
-      </when>
-    </conditional>
-    <param name="outputtype" type="select" label="Select the output format">
-        <option value="bam">bam</option>
-        <option value="sam">sam</option>
-    </param>
-  </inputs>
-  <outputs>
-    <data format="bam" name="output_bam" >
-     <change_format>
-        <when input="outputtype" value="sam" format="sam" />
-     </change_format>
-    </data>
-  </outputs>
-  <tests>
-      <test>
-          <param name="input_fastq1" value="bwa_wrapper_in2.fastqsanger" ftype="fastqsanger" />
-          <param name="input_fastq2" />
-          <param name="read_group_name" value="A" />
-          <param name="sample_name" value="unknown sample" />
-          <param name="param_type_selector" value="basic" />
-          <output name="output_bam" file="picard_fastq_to_sam_out1.bam" ftype="bam"/> 
-      </test>
-      <test>
-          <param name="input_fastq1" value="bwa_wrapper_in2.fastqsanger" ftype="fastqsanger" />
-          <param name="input_fastq2" value="bwa_wrapper_in3.fastqsanger" ftype="fastqsanger" />
-          <param name="read_group_name" value="A" />
-          <param name="sample_name" value="unknown sample" />
-          <param name="param_type_selector" value="basic" />
-          <output name="output_bam" file="picard_fastq_to_sam_out2.bam" ftype="bam"/> 
-      </test>
-  </tests>
-  <help>
-**What it does**
-
-Picard: FastqToSam converts FASTQ files to unaligned BAM files.
-
-------
-
-Please cite the website "http://picard.sourceforge.net".
-
-------
-
-
-**Input formats**
-
-FastqToSam accepts FASTQ input files (note: the Fastq-sanger file format does not work with this Picard tool). If using paired-end data, you should select two FASTQ files.
-
-------
-
-**Outputs**
-
-The output is in BAM or in SAM format, see http://samtools.sourceforge.net for more details.
-
--------
-
-**FastqToSam settings**
-
-This is list of FastqToSam options::
-
- READ_GROUP_NAME=String	Read group name Default value: A. This option can be set to 'null' to clear the default value.
- SAMPLE_NAME=String	Sample name to insert into the read group header Required.
- LIBRARY_NAME=String	The library name to place into the LB attribute in the read group header Default value: null.
- PLATFORM_UNIT=String	The platform unit (often run_barcode.lane) to insert into the read group header Default value: null.
- PLATFORM=String	The platform type (e.g. illumina, solid) to insert into the read group header Default value: null.
- SEQUENCING_CENTER=String	The sequencing center from which the data originated Default value: null.
- PREDICTED_INSERT_SIZE=Integer	Predicted median insert size, to insert into the read group header Default value: null.
- DESCRIPTION=String	Inserted into the read group header Default value: null. 
-  </help>
-</tool>