Mercurial > repos > stef > falco

changeset 25:2210b89487c6 draft

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Uploaded
author stef
date Fri, 10 Oct 2014 06:13:06 -0400
parents 4b4fba5eab4d
children 0220bfeefbc1
files falco-call.sh falco-call.xml falco-report.sh falco-report.xml falco.sh falco.xml tool_dependencies.xml
diffstat 7 files changed, 592 insertions(+), 299 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/falco-call.sh	Fri Oct 10 06:13:06 2014 -0400
@@ -0,0 +1,148 @@
+#!/bin/bash
+TOOLDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+
+echo "Start falco sh"
+
+## ----------
+## Variables setup
+## ----------
+source $1
+
+bam_base=`echo $bam_name | sed 's#.bam$##' - ` 
+
+## ----------
+## Create extra init script
+## ----------
+if [ $design_file != 'None' ] # Galaxy default is "None"
+then 
+	BED_PATH=$design_file
+else
+	BED_PATH="$TOOLDIR/tool-data/GALAXY_TSACP.bed"
+fi
+
+if [ $manifest_file != 'None' ] # Galaxy default is "None"
+then 
+	MAN_PATH=$manifest_file
+else
+	MAN_PATH="$TOOLDIR/tool-data/GALAXY_TruSeq_Amplicon_Cancer_Panel_Manifest_AFP1_PN15032433.txt"	
+fi
+
+echo "BED:"$design_file
+echo "MAN:"$manifest_file
+echo "BED chosen:"$BED_PATH
+echo "MAN chosen:"$MAN_PATH
+#echo "VARSCAN_PATH1:"$SNPEFF_JAR_PATH
+#echo "VARSCAN_PATH2:"\$SNPEFF_JAR_PATH
+
+init_file="galaxy_init.sh"
+echo '#!/bin/bash' > $init_file
+
+## executables
+#echo "snpEff=/ccagc/lib/snpEff/snpEff_v3_4" >> $init_file
+#echo "snpEff=\$SNPEFF_JAR_PATH/" >> $init_file
+#echo "snpSift=/ccagc/lib/SnpSift" >> $init_file
+#echo "snpSift=\$SNPEFF_JAR_PATH/" >> $init_file
+#echo "varscan=/ccagc/lib/VarScan/VarScan.v2.2.11.jar" >> $init_file
+#echo "varscan=\$JAVA_JAR_PATH/VarScan.v2.3.5.jar" >> $init_file
+
+## files
+echo "targetBed=$BED_PATH" >> $init_file
+echo "manifest=$MAN_PATH" >> $init_file
+
+## ----------
+## Status / debug
+## ----------
+echo "BAM: "$bam_file
+echo "OUT: "$bam_name
+echo "BAMBASE: "$bam_base
+#echo "OUTPATH: "$out_path
+#echo "HTMLOUT: "$html_out
+echo "VCFOUT : "$vcf_out
+echo "INIT   : "$init_file
+
+source $init_file
+
+echo "--- sam ---"
+samtools
+#echo "--- bcf ---"
+#bcftools
+#echo "--- snpsift ---"
+#java -jar $snpSift/SnpSift.jar
+#echo "--- snpeff ---"
+#java -jar $snpEff/snpeff.jar
+#echo "--- varscan ---"
+#java -jar $varScan
+
+exit 0
+
+## ----------
+## create output files dir
+## ----------
+mkdir $out_path
+mkdir $out_path/$bam_base
+
+## ----------
+## running analysis
+## ----------
+echo "Starting VcAn"
+$TOOLDIR/falco/amplicon-VcAn-TSACP.sh $bam_file $bam_base
+#$TOOLDIR/falco/amplicon-AlVcAn-TSACP.sh ## this contains more
+
+#echo "Starting amplicon-Report"
+#$TOOLDIR/falco/amplicon-Report.sh $bam_base
+
+#echo "Starting QC"
+#$TOOLDIR/falco/amplicon-QC.sh $bam_file
+
+#echo "Starting plots.R"
+#$TOOLDIR/falco/misc/plots.R $bam_base.qc.ann.txt $bam_base.qc.targets.txt $bam_base.pdf
+
+#echo "Starting mkHtmlReport"
+#$TOOLDIR/falco/misc/mkHtmlReport.pl ./ ./
+
+
+
+## ----------
+## create index html for main galaxy output
+## ----------
+# echo "<!DOCTYPE html>" >> $html_out
+# echo "<html>" >> $html_out
+# echo "<head>" >> $html_out
+# echo "<style>" >> $html_out
+# echo "    body{ padding: 0px 20px; }" >> $html_out
+# echo "    h1{ color: red; }" >> $html_out
+# echo "    table{ border: 1px solid black; padding: 5px }" >> $html_out
+# echo "</style>" >> $html_out
+# echo "</head>" >> $html_out
+# echo "<body>" >> $html_out
+# echo "	<h1>FALCO</h1>" >> $html_out
+# echo "	<a href=\"index.html\">HTML</a>" >> $html_out
+# echo "	<table><tbody>" >> $html_out
+# #for file in *.vcf *.txt *.tsv
+# for file in *
+# do
+# 	lineCount=`wc -l $file | cut -f 1 -d " "`
+# 	echo "	<tr><td><a href=\"$file\">$file</a> has $lineCount lines</td></tr>" >> $html_out
+# 	#echo "  <tr><td> HEAD: " `head $file` "</td></tr>" >> $html_out
+# done
+# echo "	</tbody></table>" >> $html_out
+# echo "</body>" >> $html_out
+# echo "</html>" >> $html_out
+
+## ----------
+## creating galaxy history outputs
+## ----------
+#cp 'index.html' $html_out # this is the overview of samples html
+#cp $bam_base'.html' $out_path/'out.html' # this is the sample html
+cp $bam_base'.vcf' $vcf_out
+
+## ----------
+## copy files to keep to output path
+## ----------
+#cp -r ./$bam_base/*png $out_path/$bam_base/
+#cp -r ./* $out_path
+#cp *.vcf $out_path; cp *.tsv $out_path; cp *.txt $out_path; cp *.html $out_path
+
+## ----------
+echo "END falco sh"
+exit 0
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/falco-call.xml	Fri Oct 10 06:13:06 2014 -0400
@@ -0,0 +1,137 @@
+<tool id="falco-call" name="falco-call" version="0.0.1">
+  
+  <requirements>
+    
+    <requirement type="package" version="0.1.19">samtools</requirement>
+
+    <requirement type="package" version="3.1.0">R</requirement>
+    <!--
+    <requirement type="package" version="3.4">snpeff</requirement>
+    <requirement type="package" version="2">varscan</requirement> 
+    <requirement type="package" version="2">bcftools</requirement> 
+    -->
+    <!--
+    
+    <requirement type="set_environment">JAVA_JAR_PATH</requirement>
+    <requirement type="set_environment">SNPEFF_JAR_PATH</requirement>
+    
+    <requirement type="set_environment">JAR_PATH1</requirement>
+    <requirement type="set_environment">JAR_PATH2</requirement>
+    -->
+    <requirement type="set_environment">TOOL_DIR</requirement>
+    
+  </requirements>
+
+  <description>FALCO: Amplicon Analysis Pipeline</description>
+  
+  <!-- command block to call script with specific R installation (set full paths) -->
+  <!--
+  <command>
+    /full/path/to/Rscript 
+    /full/path/to/QDNAseq.R 
+    $qdnaseq_cfg
+  </command>
+  -->
+
+  <!-- command block to call script with default R environment -->
+  <command interpreter="bash">
+    <!--falco.sh $bam $bam.name $html_output $vcf_output ${html_output.files_path} &amp;&amp;; echo "ECHO PRINT"; -->
+    <!-- falco.sh $falco_cfg \$JAVA_JAR_PATH \$SNPEFF_JAR_PATH; -->
+    falco-call.sh $falco_cfg;
+  </command>
+  <!--
+  <command interpreter="bash">
+    falco/amplicon-VcAn-TSACP.sh $bam $bam.name;
+    echo "DONE"
+  </command>
+  <command interpreter="perl">
+    falco.pl $htmlFile ${htmlFile.files_path} $bam $bam.name;
+  </command>
+  -->
+
+  <stdio>
+    <!-- Anything higher than 0 means the bash script didnt finish -->
+    <exit_code range="1:" level="fatal" description="Bash script didnt finish correctly, check log" />
+  </stdio>
+  
+  <inputs>
+    <!-- ==================== -->
+    <!-- General inputs -->
+    <!-- ==================== -->
+    <param name="jobName" type="text" optional="false" label="Analysis/ouput name" help="Supply a name for the outputs to remind you what they contain" value="TEST">
+      <validator type="empty_field" />
+      <validator type="regex" message="This field may contain only non-whitespace characters">\S+</validator>
+    </param>
+    <param name="bam" type="data" multiple="false" optional="false" format="bam" label="Input BAM" help="Select BAM file" />
+
+    <param format="fasta" name="reference" type="data" metadata_name="dbkey" label="Reference File"/>
+    <param format="bed" name="design_file" optional="True" type="data" label="BED File" help="When left empty, default Cancer Panel is used"/>
+    <param format="txt" name="manifest_file" optional="True" type="data" label="MANIFEST File" help="When left empty, default Cancer Panel is used"/>
+
+    <!-- ==================== -->
+    <!-- Option to use your own bin annotations -->
+    <!-- ==================== -->
+  
+  </inputs>
+  
+  <!-- ==================== -->
+  <!-- This config is sourced by tool -->
+  <!-- ==================== -->
+  <configfiles>
+    <configfile name="falco_cfg">
+      design_file=$design_file
+      manifest_file=$manifest_file
+      bam_file=$bam
+      bam_name=$bam.name
+      <!--html_out=$html_output-->
+      vcf_out=$vcf_output
+      out_path=${vcf_output.files_path}
+    </configfile>
+  </configfiles>
+      <!--
+      jar_path1=$JAR_PATH1
+      jar_path2=$JAR_PATH2
+      jar_path3=$JAVA_JAR_PATH
+      jar_path4=$SNPEFF_JAR_PATH
+    -->
+  <!-- ==================== -->
+  <!-- Main output is an html based report, additional on request -->
+  <!-- ==================== -->
+  <outputs>
+    <!--<data format="html" name="html_output" label="FALCO AAP (${jobName})" />-->
+    <data format="vcf" name="vcf_output" label="FALCO AAP (${jobName}): VCF" />
+  </outputs>
+
+  <!-- ==================== -->
+  <!-- Tests still to be done -->
+  <!-- ==================== -->
+
+  <!-- 
+  <tests>
+    <test>
+      <param name="input1" value="input1" />   
+      <param name="input2" value="input2" />   
+    </test>
+  </tests>
+  -->
+
+  <help>
+.. class:: infomark
+
+**Introduction**
+
+This tool is a wrapper for the Amplicon Analysis Pipeline (AAP) FALCO_
+
+.. _FALCO: https://bitbucket.org/daoud/falco
+
+Calls and annotates genomic variants for each amplicon in a design.
+
+-----
+
+**Citation**
+
+For the underlying tool please cite: Daoud Sie et al. Performance of amplicon-based next generation DNA sequencing for diagnostic gene mutation profiling in oncopathology (Cell Oncol 2014 Oct;37(5):353-61).
+
+  </help>
+
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/falco-report.sh	Fri Oct 10 06:13:06 2014 -0400
@@ -0,0 +1,159 @@
+#!/bin/bash
+TOOLDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+
+echo "Start falco sh"
+
+## ----------
+## Variables setup
+## ----------
+#bam_file=$1
+#bam_name=$2
+#html_out=$3
+#vcf_out=$4
+#out_path=$5
+source $1
+JAR_PATH=$2
+#JAR_PATH=$3
+
+bam_base=`echo $bam_name | sed 's#.bam$##' - ` 
+
+## ----------
+## Create extra init script
+## ----------
+#if [ $design_file != 'None' && $design_file != '' ]; then BED_PATH=$design_file; fi
+#if [ $manifest_file != 'None' && $manifest_file != '' ]; then MAN_PATH=$manifest_file; fi
+if [ $design_file != 'None' ] # Galaxy default is "None"
+then 
+	BED_PATH=$design_file
+else
+	BED_PATH="$TOOLDIR/tool-data/GALAXY_TSACP.bed"
+fi
+
+if [ $manifest_file != 'None' ] # Galaxy default is "None"
+then 
+	MAN_PATH=$manifest_file
+else
+	MAN_PATH="$TOOLDIR/tool-data/GALAXY_TruSeq_Amplicon_Cancer_Panel_Manifest_AFP1_PN15032433.txt"	
+fi
+
+echo "BED:"$design_file
+echo "MAN:"$manifest_file
+echo "BED chosen:"$BED_PATH
+echo "MAN chosen:"$MAN_PATH
+#echo "VARSCAN_PATH1:"$SNPEFF_JAR_PATH
+#echo "VARSCAN_PATH2:"\$SNPEFF_JAR_PATH
+echo "JAR_PATH1:"$JAR_PATH
+#echo "JAR_PATH2:"$jar_path2
+
+init_file="galaxy_init.sh"
+echo '#!/bin/bash' > $init_file
+
+## executables
+#echo "snpEff=/ccagc/lib/snpEff/snpEff_v3_4" >> $init_file
+echo "snpEff=\$SNPEFF_JAR_PATH/" >> $init_file
+#echo "snpSift=/ccagc/lib/SnpSift" >> $init_file
+echo "snpSift=\$SNPEFF_JAR_PATH/" >> $init_file
+#echo "varscan=/ccagc/lib/VarScan/VarScan.v2.2.11.jar" >> $init_file
+echo "varscan=\$JAVA_JAR_PATH/VarScan.v2.3.5.jar" >> $init_file
+
+## files
+echo "targetBed=$BED_PATH" >> $init_file
+echo "manifest=$MAN_PATH" >> $init_file
+
+## ----------
+## Status / debug
+## ----------
+echo "BAM: "$bam_file
+echo "OUT: "$bam_name
+echo "BAMBASE: "$bam_base
+echo "OUTPATH: "$out_path
+echo "HTMLOUT: "$html_out
+echo "VCFOUT : "$vcf_out
+echo "INIT   : "$init_file
+
+source $init_file
+
+echo "--- sam ---"
+samtools
+echo "--- bcf ---"
+bcftools
+echo "--- snpsift ---"
+java -jar $snpSift/SnpSift.jar
+echo "--- snpeff ---"
+java -jar $snpEff/snpeff.jar
+echo "--- varscan ---"
+java -jar $varScan
+
+exit 0
+
+## ----------
+## create output files dir
+## ----------
+mkdir $out_path
+mkdir $out_path/$bam_base
+
+## ----------
+## running analysis
+## ----------
+echo "Starting VcAn"
+$TOOLDIR/falco/amplicon-VcAn-TSACP.sh $bam_file $bam_base
+#$TOOLDIR/falco/amplicon-AlVcAn-TSACP.sh ## this contains more
+
+echo "Starting amplicon-Report"
+$TOOLDIR/falco/amplicon-Report.sh $bam_base
+
+echo "Starting QC"
+$TOOLDIR/falco/amplicon-QC.sh $bam_file
+
+#echo "Starting plots.R"
+#$TOOLDIR/falco/misc/plots.R $bam_base.qc.ann.txt $bam_base.qc.targets.txt $bam_base.pdf
+
+echo "Starting mkHtmlReport"
+$TOOLDIR/falco/misc/mkHtmlReport.pl ./ ./
+
+
+
+## ----------
+## create index html for main galaxy output
+## ----------
+echo "<!DOCTYPE html>" >> $html_out
+echo "<html>" >> $html_out
+echo "<head>" >> $html_out
+echo "<style>" >> $html_out
+echo "    body{ padding: 0px 20px; }" >> $html_out
+echo "    h1{ color: red; }" >> $html_out
+echo "    table{ border: 1px solid black; padding: 5px }" >> $html_out
+echo "</style>" >> $html_out
+echo "</head>" >> $html_out
+echo "<body>" >> $html_out
+echo "	<h1>FALCO</h1>" >> $html_out
+echo "	<a href=\"index.html\">HTML</a>" >> $html_out
+echo "	<table><tbody>" >> $html_out
+#for file in *.vcf *.txt *.tsv
+for file in *
+do
+	lineCount=`wc -l $file | cut -f 1 -d " "`
+	echo "	<tr><td><a href=\"$file\">$file</a> has $lineCount lines</td></tr>" >> $html_out
+	#echo "  <tr><td> HEAD: " `head $file` "</td></tr>" >> $html_out
+done
+echo "	</tbody></table>" >> $html_out
+echo "</body>" >> $html_out
+echo "</html>" >> $html_out
+
+## ----------
+## creating galaxy history outputs
+## ----------
+#cp 'index.html' $html_out # this is the overview of samples html
+cp $bam_base'.html' $out_path/'out.html' # this is the sample html
+cp $bam_base'.vcf' $vcf_out
+
+## ----------
+## copy files to keep to output path
+## ----------
+cp -r ./$bam_base/*png $out_path/$bam_base/
+cp -r ./* $out_path
+#cp *.vcf $out_path; cp *.tsv $out_path; cp *.txt $out_path; cp *.html $out_path
+
+## ----------
+echo "END falco sh"
+exit 0
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/falco-report.xml	Fri Oct 10 06:13:06 2014 -0400
@@ -0,0 +1,137 @@
+<tool id="falco-report" name="falco-report" version="0.0.1">
+  
+  <requirements>
+    
+    <requirement type="package" version="0.1.19">samtools</requirement>
+
+    <requirement type="package" version="3.1.0">R</requirement>
+    <!--
+    <requirement type="package" version="3.4">snpeff</requirement>
+    <requirement type="package" version="2">varscan</requirement> 
+    <requirement type="package" version="2">bcftools</requirement> 
+    -->
+    <!--
+    
+    <requirement type="set_environment">JAVA_JAR_PATH</requirement>
+    <requirement type="set_environment">SNPEFF_JAR_PATH</requirement>
+    
+    <requirement type="set_environment">JAR_PATH1</requirement>
+    <requirement type="set_environment">JAR_PATH2</requirement>
+    -->
+    <requirement type="set_environment">TOOL_DIR</requirement>
+    
+  </requirements>
+
+  <description>FALCO: Amplicon Analysis Pipeline</description>
+  
+  <!-- command block to call script with specific R installation (set full paths) -->
+  <!--
+  <command>
+    /full/path/to/Rscript 
+    /full/path/to/QDNAseq.R 
+    $qdnaseq_cfg
+  </command>
+  -->
+
+  <!-- command block to call script with default R environment -->
+  <command interpreter="bash">
+    <!--falco.sh $bam $bam.name $html_output $vcf_output ${html_output.files_path} &amp;&amp;; echo "ECHO PRINT"; -->
+    <!-- falco.sh $falco_cfg \$JAVA_JAR_PATH \$SNPEFF_JAR_PATH; -->
+    falco-report.sh $falco_cfg;
+  </command>
+  <!--
+  <command interpreter="bash">
+    falco/amplicon-VcAn-TSACP.sh $bam $bam.name;
+    echo "DONE"
+  </command>
+  <command interpreter="perl">
+    falco.pl $htmlFile ${htmlFile.files_path} $bam $bam.name;
+  </command>
+  -->
+
+  <stdio>
+    <!-- Anything higher than 0 means the bash script didnt finish -->
+    <exit_code range="1:" level="fatal" description="Bash script didnt finish correctly, check log" />
+  </stdio>
+  
+  <inputs>
+    <!-- ==================== -->
+    <!-- General inputs -->
+    <!-- ==================== -->
+    <param name="jobName" type="text" optional="false" label="Analysis/ouput name" help="Supply a name for the outputs to remind you what they contain" value="TEST">
+      <validator type="empty_field" />
+      <validator type="regex" message="This field may contain only non-whitespace characters">\S+</validator>
+    </param>
+    <param name="bam" type="data" multiple="false" optional="false" format="bam" label="Input BAM" help="Select BAM file" />
+
+    <param format="fasta" name="reference" type="data" metadata_name="dbkey" label="Reference File"/>
+    <param format="bed" name="design_file" optional="True" type="data" label="BED File" help="When left empty, default Cancer Panel is used"/>
+    <param format="txt" name="manifest_file" optional="True" type="data" label="MANIFEST File" help="When left empty, default Cancer Panel is used"/>
+
+    <!-- ==================== -->
+    <!-- Option to use your own bin annotations -->
+    <!-- ==================== -->
+  
+  </inputs>
+  
+  <!-- ==================== -->
+  <!-- This config is sourced by tool -->
+  <!-- ==================== -->
+  <configfiles>
+    <configfile name="falco_cfg">
+      design_file=$design_file
+      manifest_file=$manifest_file
+      bam_file=$bam
+      bam_name=$bam.name
+      <!--html_out=$html_output-->
+      vcf_out=$vcf_output
+      out_path=${vcf_output.files_path}
+    </configfile>
+  </configfiles>
+      <!--
+      jar_path1=$JAR_PATH1
+      jar_path2=$JAR_PATH2
+      jar_path3=$JAVA_JAR_PATH
+      jar_path4=$SNPEFF_JAR_PATH
+    -->
+  <!-- ==================== -->
+  <!-- Main output is an html based report, additional on request -->
+  <!-- ==================== -->
+  <outputs>
+    <!--<data format="html" name="html_output" label="FALCO AAP (${jobName})" />-->
+    <data format="vcf" name="vcf_output" label="FALCO AAP (${jobName}): VCF" />
+  </outputs>
+
+  <!-- ==================== -->
+  <!-- Tests still to be done -->
+  <!-- ==================== -->
+
+  <!-- 
+  <tests>
+    <test>
+      <param name="input1" value="input1" />   
+      <param name="input2" value="input2" />   
+    </test>
+  </tests>
+  -->
+
+  <help>
+.. class:: infomark
+
+**Introduction**
+
+This tool is a wrapper for the Amplicon Analysis Pipeline (AAP) FALCO_
+
+.. _FALCO: https://bitbucket.org/daoud/falco
+
+Calls and annotates genomic variants for each amplicon in a design.
+
+-----
+
+**Citation**
+
+For the underlying tool please cite: Daoud Sie et al. Performance of amplicon-based next generation DNA sequencing for diagnostic gene mutation profiling in oncopathology (Cell Oncol 2014 Oct;37(5):353-61).
+
+  </help>
+
+</tool>
--- a/falco.sh	Wed Oct 08 08:14:41 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,159 +0,0 @@
-#!/bin/bash
-TOOLDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
-
-echo "Start falco sh"
-
-## ----------
-## Variables setup
-## ----------
-#bam_file=$1
-#bam_name=$2
-#html_out=$3
-#vcf_out=$4
-#out_path=$5
-source $1
-JAR_PATH=$2
-#JAR_PATH=$3
-
-bam_base=`echo $bam_name | sed 's#.bam$##' - ` 
-
-## ----------
-## Create extra init script
-## ----------
-#if [ $design_file != 'None' && $design_file != '' ]; then BED_PATH=$design_file; fi
-#if [ $manifest_file != 'None' && $manifest_file != '' ]; then MAN_PATH=$manifest_file; fi
-if [ $design_file != 'None' ] # Galaxy default is "None"
-then 
-	BED_PATH=$design_file
-else
-	BED_PATH="$TOOLDIR/tool-data/GALAXY_TSACP.bed"
-fi
-
-if [ $manifest_file != 'None' ] # Galaxy default is "None"
-then 
-	MAN_PATH=$manifest_file
-else
-	MAN_PATH="$TOOLDIR/tool-data/GALAXY_TruSeq_Amplicon_Cancer_Panel_Manifest_AFP1_PN15032433.txt"	
-fi
-
-echo "BED:"$design_file
-echo "MAN:"$manifest_file
-echo "BED chosen:"$BED_PATH
-echo "MAN chosen:"$MAN_PATH
-#echo "VARSCAN_PATH1:"$SNPEFF_JAR_PATH
-#echo "VARSCAN_PATH2:"\$SNPEFF_JAR_PATH
-echo "JAR_PATH1:"$JAR_PATH
-#echo "JAR_PATH2:"$jar_path2
-
-init_file="galaxy_init.sh"
-echo '#!/bin/bash' > $init_file
-
-## executables
-#echo "snpEff=/ccagc/lib/snpEff/snpEff_v3_4" >> $init_file
-echo "snpEff=\$SNPEFF_JAR_PATH/" >> $init_file
-#echo "snpSift=/ccagc/lib/SnpSift" >> $init_file
-echo "snpSift=\$SNPEFF_JAR_PATH/" >> $init_file
-#echo "varscan=/ccagc/lib/VarScan/VarScan.v2.2.11.jar" >> $init_file
-echo "varscan=\$JAVA_JAR_PATH/VarScan.v2.3.5.jar" >> $init_file
-
-## files
-echo "targetBed=$BED_PATH" >> $init_file
-echo "manifest=$MAN_PATH" >> $init_file
-
-## ----------
-## Status / debug
-## ----------
-echo "BAM: "$bam_file
-echo "OUT: "$bam_name
-echo "BAMBASE: "$bam_base
-echo "OUTPATH: "$out_path
-echo "HTMLOUT: "$html_out
-echo "VCFOUT : "$vcf_out
-echo "INIT   : "$init_file
-
-source $init_file
-
-echo "--- sam ---"
-samtools
-echo "--- bcf ---"
-bcftools
-echo "--- snpsift ---"
-java -jar $snpSift/SnpSift.jar
-echo "--- snpeff ---"
-java -jar $snpEff/snpeff.jar
-echo "--- varscan ---"
-java -jar $varScan
-
-exit 0
-
-## ----------
-## create output files dir
-## ----------
-mkdir $out_path
-mkdir $out_path/$bam_base
-
-## ----------
-## running analysis
-## ----------
-echo "Starting VcAn"
-$TOOLDIR/falco/amplicon-VcAn-TSACP.sh $bam_file $bam_base
-#$TOOLDIR/falco/amplicon-AlVcAn-TSACP.sh ## this contains more
-
-echo "Starting amplicon-Report"
-$TOOLDIR/falco/amplicon-Report.sh $bam_base
-
-echo "Starting QC"
-$TOOLDIR/falco/amplicon-QC.sh $bam_file
-
-#echo "Starting plots.R"
-#$TOOLDIR/falco/misc/plots.R $bam_base.qc.ann.txt $bam_base.qc.targets.txt $bam_base.pdf
-
-echo "Starting mkHtmlReport"
-$TOOLDIR/falco/misc/mkHtmlReport.pl ./ ./
-
-
-
-## ----------
-## create index html for main galaxy output
-## ----------
-echo "<!DOCTYPE html>" >> $html_out
-echo "<html>" >> $html_out
-echo "<head>" >> $html_out
-echo "<style>" >> $html_out
-echo "    body{ padding: 0px 20px; }" >> $html_out
-echo "    h1{ color: red; }" >> $html_out
-echo "    table{ border: 1px solid black; padding: 5px }" >> $html_out
-echo "</style>" >> $html_out
-echo "</head>" >> $html_out
-echo "<body>" >> $html_out
-echo "	<h1>FALCO</h1>" >> $html_out
-echo "	<a href=\"index.html\">HTML</a>" >> $html_out
-echo "	<table><tbody>" >> $html_out
-#for file in *.vcf *.txt *.tsv
-for file in *
-do
-	lineCount=`wc -l $file | cut -f 1 -d " "`
-	echo "	<tr><td><a href=\"$file\">$file</a> has $lineCount lines</td></tr>" >> $html_out
-	#echo "  <tr><td> HEAD: " `head $file` "</td></tr>" >> $html_out
-done
-echo "	</tbody></table>" >> $html_out
-echo "</body>" >> $html_out
-echo "</html>" >> $html_out
-
-## ----------
-## creating galaxy history outputs
-## ----------
-#cp 'index.html' $html_out # this is the overview of samples html
-cp $bam_base'.html' $out_path/'out.html' # this is the sample html
-cp $bam_base'.vcf' $vcf_out
-
-## ----------
-## copy files to keep to output path
-## ----------
-cp -r ./$bam_base/*png $out_path/$bam_base/
-cp -r ./* $out_path
-#cp *.vcf $out_path; cp *.tsv $out_path; cp *.txt $out_path; cp *.html $out_path
-
-## ----------
-echo "END falco sh"
-exit 0
\ No newline at end of file
--- a/falco.xml	Wed Oct 08 08:14:41 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,132 +0,0 @@
-<tool id="falco" name="falco" version="0.0.1">
-  
-  <requirements>
-    
-    <requirement type="package" version="0.1.19">samtools</requirement>
-    <requirement type="package" version="3.0.3">R</requirement>
-    <requirement type="package" version="3.4">snpeff</requirement>
-    <requirement type="package" version="2">varscan</requirement> 
-    <requirement type="package" version="2">bcftools</requirement> 
-    <!--
-    
-    <requirement type="set_environment">JAVA_JAR_PATH</requirement>
-    <requirement type="set_environment">SNPEFF_JAR_PATH</requirement>
-    -->
-    <requirement type="set_environment">JAR_PATH1</requirement>
-    <requirement type="set_environment">JAR_PATH2</requirement>
-    <requirement type="set_environment">TOOL_DIR</requirement>
-  </requirements>
-
-  <description>FALCO: Amplicon Analysis Pipeline</description>
-  
-  <!-- command block to call script with specific R installation (set full paths) -->
-  <!--
-  <command>
-    /full/path/to/Rscript 
-    /full/path/to/QDNAseq.R 
-    $qdnaseq_cfg
-  </command>
-  -->
-
-  <!-- command block to call script with default R environment -->
-  <command interpreter="bash">
-    <!--falco.sh $bam $bam.name $html_output $vcf_output ${html_output.files_path} &amp;&amp;; echo "ECHO PRINT"; -->
-    <!-- falco.sh $falco_cfg \$JAVA_JAR_PATH \$SNPEFF_JAR_PATH; -->
-    falco.sh $falco_cfg \$SNPEFF_JAR_PATH;
-  </command>
-  <!--
-  <command interpreter="bash">
-    falco/amplicon-VcAn-TSACP.sh $bam $bam.name;
-    echo "DONE"
-  </command>
-  <command interpreter="perl">
-    falco.pl $htmlFile ${htmlFile.files_path} $bam $bam.name;
-  </command>
-  -->
-
-  <stdio>
-    <!-- Anything higher than 0 means the bash script didnt finish -->
-    <exit_code range="1:" level="fatal" description="Bash script didnt finish correctly, check log" />
-  </stdio>
-  
-  <inputs>
-    <!-- ==================== -->
-    <!-- General inputs -->
-    <!-- ==================== -->
-    <param name="jobName" type="text" optional="false" label="Analysis/ouput name" help="Supply a name for the outputs to remind you what they contain" value="TEST">
-      <validator type="empty_field" />
-      <validator type="regex" message="This field may contain only non-whitespace characters">\S+</validator>
-    </param>
-    <param name="bam" type="data" multiple="false" optional="false" format="bam" label="Input BAM" help="Select BAM file" />
-
-    <param format="fasta" name="reference" type="data" metadata_name="dbkey" label="Reference File"/>
-    <param format="bed" name="design_file" optional="True" type="data" label="BED File" help="When left empty, default Cancer Panel is used"/>
-    <param format="txt" name="manifest_file" optional="True" type="data" label="MANIFEST File" help="When left empty, default Cancer Panel is used"/>
-
-    <!-- ==================== -->
-    <!-- Option to use your own bin annotations -->
-    <!-- ==================== -->
-  
-  </inputs>
-  
-  <!-- ==================== -->
-  <!-- This config is sourced by tool -->
-  <!-- ==================== -->
-  <configfiles>
-    <configfile name="falco_cfg">
-      design_file=$design_file
-      manifest_file=$manifest_file
-      bam_file=$bam
-      bam_name=$bam.name
-      html_out=$html_output
-      vcf_out=$vcf_output
-      out_path=${html_output.files_path}
-    </configfile>
-  </configfiles>
-      <!--
-      jar_path1=$JAR_PATH1
-      jar_path2=$JAR_PATH2
-      jar_path3=$JAVA_JAR_PATH
-      jar_path4=$SNPEFF_JAR_PATH
-    -->
-  <!-- ==================== -->
-  <!-- Main output is an html based report, additional on request -->
-  <!-- ==================== -->
-  <outputs>
-    <data format="html" name="html_output" label="FALCO AAP (${jobName})" />
-    <data format="vcf" name="vcf_output" label="FALCO AAP (${jobName}): VCF" />
-  </outputs>
-
-  <!-- ==================== -->
-  <!-- Tests still to be done -->
-  <!-- ==================== -->
-
-  <!-- 
-  <tests>
-    <test>
-      <param name="input1" value="input1" />   
-      <param name="input2" value="input2" />   
-    </test>
-  </tests>
-  -->
-
-  <help>
-.. class:: infomark
-
-**Introduction**
-
-This tool is a wrapper for the Amplicon Analysis Pipeline (AAP) FALCO_
-
-.. _FALCO: https://bitbucket.org/daoud/falco
-
-Calls and annotates genomic variants for each amplicon in a design.
-
------
-
-**Citation**
-
-For the underlying tool please cite: Daoud Sie et al. Title TBA (submitted).
-
-  </help>
-
-</tool>
--- a/tool_dependencies.xml	Wed Oct 08 08:14:41 2014 -0400
+++ b/tool_dependencies.xml	Fri Oct 10 06:13:06 2014 -0400
@@ -2,42 +2,45 @@
 <tool_dependency>
     
     <!-- PACKAGES -->
-    <package name="R" version="3.0.3">
-        <repository changeset_revision="9ff23e0b280b" name="package_r_3_0_3" owner="iuc" prior_installation_required="TRUE" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-        <readme>Let's see where this msg appears...R</readme>
+    <package name="R" version="3.1.0">
+        <repository changeset_revision="a6cc7706ea14" name="package_r_3_1_0" owner="iuc" prior_installation_required="TRUE" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     
     <package name="samtools" version="0.1.19">
         <repository changeset_revision="233326db3402" name="package_samtools_0_1_19" owner="devteam" prior_installation_required="TRUE" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-        <readme>Let's see where this msg appears...samtools</readme>
     </package>
 
+    <!--
     <package name="bcftools" version="2">
-        <repository changeset_revision="5f9ba601748e" name="bcftools" owner="iuc" prior_installation_required="TRUE" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository name="bcftools" owner="iuc" prior_installation_required="TRUE" />
         <readme>Let's see where this msg appears...bcftools</readme>
     </package>
     
     <package name="snpeff" version="3.4">
-        <repository changeset_revision="7fb1061d905a" name="package_snpeff_3_4" owner="jjohnson" prior_installation_required="TRUE" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository name="package_snpeff_3_4" owner="jjohnson" prior_installation_required="TRUE" />
         <readme>Let's see where this msg appears...snpeff</readme>
     </package>
     
     <package name="varscan" version="2">
-        <repository changeset_revision="f82940004c84" name="varscan_version_2" owner="devteam" prior_installation_required="TRUE" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository name="varscan_version_2" owner="devteam" prior_installation_required="TRUE" />
         <readme>Let's see where this msg appears...varscan</readme>
     </package>
+    -->
     
     <!-- ENV -->
+    
     <set_environment>
         <environment_variable action="set_to" name="TOOL_DIR">$REPOSITORY_INSTALL_DIR</environment_variable>
     </set_environment>
+    <!--
     <set_environment>
         <environment_variable action="set_to" name="JAR_PATH1">$JAVA_JAR_PATH</environment_variable>
     </set_environment>
     <set_environment>
         <environment_variable action="set_to" name="JAR_PATH2">$SNPEFF_JAR_PATH</environment_variable>
     </set_environment>
-    
+    -->
+
     <!--<environment_variable action="set_to" name="VARSCAN_DIR">$JAVA_JAR_PATH</environment_variable>-->
     
 </tool_dependency>