--- a/defuse.xml	Tue Nov 08 13:56:35 2011 -0600
+++ b/defuse.xml	Fri Jan 06 16:06:17 2012 -0600
@@ -1,18 +1,9 @@
-<tool id="defuse" name="DeFuse" version="1.1">
+<tool id="defuse" name="DeFuse" version="1.2">
  <description>identify fusion transcripts</description>
  <requirements>
   <requirement type="binary"></requirement>
  </requirements>
- <command interpreter="perl">
-  ## Find the defuse.pl in the galaxy tool path
-  #import Cheetah.FileUtils
-  #set $toolpath = '/'.join([$__root_dir__,'tools','defuse'])
-  #set $defuse = $Cheetah.FileUtils.findFiles($toolpath,['defuse.pl'],[],['tools','external','include','em','data'])[0]
-  $defuse
-  -c `cp $defuse_config $config_txt; echo $defuse_config`
-  -d `mkdir -p data_dir; ln -s $left_pairendreads data_dir/reads_1.fastq; ln -s $right_pairendreads data_dir/reads_2.fastq; echo data_dir`
-  -o  output_dir -p 8
- </command>
+  <command interpreter="command"> /bin/bash $shscript </command>
  <inputs>
   <param name="left_pairendreads" type="data" format="fastq" label="left part of read pairs" help="The left and right reads pairs must be in the same order, and not have any unpaired reads.  (FASTQ interlacer will pair reads and remove the unpaired.   FASTQ de-interlacer will separate the result into left and right reads.)"/>
   <param name="right_pairendreads" type="data" format="fastq" label="right part of read pairs" help="In the same order as the left reads"/>
@@ -77,6 +68,8 @@
         <param name="config" type="data" format="txt" label="Defuse Config file" help=""/>
       </when>  <!-- history -->
   </conditional>  <!-- refGenomeSource -->
+  <param name="keep_output" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Save DeFuse working directory files"/>
+  <param name="do_get_reads" type="boolean" checked="false" truevalue="yes" falsevalue="no" label="Run get_reads on each cluster"/>
  </inputs>
  <configfiles>
   <configfile name="defuse_config">
@@ -243,7 +236,7 @@
 #try
 $ref_dict['bowtie_threads']
 #except
-1
+4
 #end try
 bowtie_quals = #slurp
 #try
@@ -502,13 +495,103 @@
 #end if
 
   </configfile>
+  <configfile name="shscript">
+#!/bin/bash
+## define some things for cheetah proccessing
+#set $ds = chr(36)
+#set $gt = chr(62)
+#set $lt = chr(60)
+#set $echo_cmd = 'echo'
+## Find the defuse.pl in the galaxy tool path
+#import Cheetah.FileUtils
+#set $toolpath = '/'.join([$__root_dir__,'tools','defuse'])
+#set $defuse = $Cheetah.FileUtils.findFiles($toolpath,['defuse.pl'],[],['tools','external','include','em','data'])[0]
+#set $get_reads = $Cheetah.FileUtils.findFiles($toolpath,['get_reads.pl'],[],['tools','external','include','em','data'])[0]
+## declare a bash function for converting a results tsv into html with links to the get_reads output files
+results2html() {
+  rlts=${ds}1
+  rslt_name=`basename ${ds}rlts`
+  html=${ds}2
+  echo '${lt}html${gt}${lt}head${gt}${lt}title${gt}Defuse '${ds}rslt_name'${lt}/title${gt}${lt}/head${gt}${lt}body${gt}' ${gt}  ${ds}html
+  echo '${lt}h2${gt}Defuse '${ds}rslt_name'${lt}/h2${gt}${lt}table${gt}' ${gt}${gt}  ${ds}html
+  if [ -z "${ds}3" ]  
+  then
+    awk '${ds}1 ~ /cluster_id/{printf("${lt}tr${gt}");for (i = 1; i ${lt}= NF; i++) {printf("${lt}th${gt}%s${lt}/th${gt}", ${ds}i);}; printf("${lt}/tr${gt}\n");}\
+         ${ds}1 ~ /[1-9][0-9]*/{printf("${lt}tr${gt}");for (i = 1; i ${lt}= NF; i++) {printf("${lt}td${gt}%s${lt}/td${gt}", ${ds}i);}; printf("${lt}/tr${gt}\n");}' ${ds}rlts ${gt}${gt} ${ds}html
+    echo '${lt}/table${gt}' ${gt}${gt} ${ds}html
+    echo '${lt}/body${gt}${lt}/html${gt}' ${gt}${gt}  ${ds}html
+  else
+    export _EFP=${ds}3
+    mkdir -p ${ds}_EFP
+    awk '${ds}1 ~ /cluster_id/{printf("${lt}tr${gt}");for (i = 1; i ${lt}= NF; i++) {printf("${lt}th${gt}%s${lt}/th${gt}", ${ds}i);}; printf("${lt}/tr${gt}\n");}\
+         ${ds}1 ~ /[1-9][0-9]*/{fn="cluster_"${ds}1"_reads.txt"; \
+          printf("${lt}tr${gt}${lt}td${gt}${lt}a href=\"%s\"${gt}%s${lt}/a${gt}${lt}/td${gt}",fn, ${ds}1);for (i = 2; i ${lt}= NF; i++) {printf("${lt}td${gt}%s${lt}/td${gt}", ${ds}i);}; printf("${lt}/tr${gt}\n");}' ${ds}rlts ${gt}${gt} ${ds}html
+    echo '${lt}/table${gt}' ${gt}${gt} ${ds}html
+    echo '${lt}/body${gt}${lt}/html${gt}' ${gt}${gt}  ${ds}html
+    for i in `awk '${ds}1 ~ /[1-9][0-9]*/{print ${ds}1}' ${ds}rlts`;
+      do fn=cluster_${ds}{i}_reads.txt;
+      pn=${ds}_EFP/${ds}fn;
+      perl $get_reads -c $defuse_config -o output_dir -i ${ds}i ${gt} ${ds}pn;
+    done
+  fi
+}
+## copy config to output
+cp $defuse_config $config_txt
+## make a data_dir  and ln -s the input fastq
+mkdir -p data_dir
+ln -s $left_pairendreads data_dir/reads_1.fastq
+ln -s $right_pairendreads data_dir/reads_2.fastq
+## ln to output_dir in from_work_dir
+#if $defuse_out.__str__ != 'None':
+mkdir -p $defuse_out.extra_files_path
+ln -s $defuse_out.extra_files_path  output_dir
+#else
+mkdir -p output_dir
+#end if
+## run defuse.pl
+perl $defuse -c $defuse_config -d data_dir -o output_dir  -p 8
+## copy primary results to output datasets
+if [ -e output_dir/log/defuse.log ]; then cp output_dir/log/defuse.log $defuse_log; fi
+if [ -e output_dir/results.tsv ]; then cp output_dir/results.tsv $results_tsv; fi
+if [ -e output_dir/results.filtered.tsv ]; then cp output_dir/results.filtered.tsv $results_filtered_tsv; fi
+if [ -e output_dir/results.classify.tsv ]; then cp output_dir/results.classify.tsv $results_classify_tsv; fi
+## create html with links for output_dir
+#if $defuse_out.__str__ != 'None':
+if [ -e $defuse_out ]
+then
+  echo '${lt}html${gt}${lt}head${gt}${lt}title${gt}Defuse Output${lt}/title${gt}${lt}/head${gt}${lt}body${gt}' ${gt} $defuse_out
+  echo '${lt}h2${gt}Defuse Output Files${lt}/h2${gt}${lt}ul${gt}' ${gt}${gt}  $defuse_out
+  pushd $defuse_out.extra_files_path
+  for f in `find -L . -maxdepth 1 -type f`; 
+   do fn=`basename ${ds}f`; echo '${lt}li${gt}${lt}a href="'${ds}fn'"${gt}'${ds}fn'${lt}/a${gt}${lt}/li${gt}' ${gt}${gt}  $defuse_out; 
+  done
+  popd
+  echo '${lt}/ul${gt}' ${gt}${gt} $defuse_out
+  echo '${lt}/body${gt}${lt}/html${gt}' ${gt}${gt}  $defuse_out
+fi
+#end if
+## run get_reads.pl on each cluster
+#if $fusion_reads.__str__ != 'None':
+if [ -e output_dir/results.filtered.tsv -a -e $fusion_reads ] 
+then
+  mkdir -p $fusion_reads.extra_files_path
+  results2html output_dir/results.filtered.tsv $fusion_reads $fusion_reads.extra_files_path
+fi
+#end if
+  </configfile>
  </configfiles>
  <outputs>
   <data format="txt" name="config_txt" label="${tool.name} on ${on_string}: config.txt"/>
-  <data format="txt" name="defuse_log" label="${tool.name} on ${on_string}: defuse.log" from_work_dir="output_dir/log/defuse.log"/>
-  <data format="tabular" name="results_tsv" label="${tool.name} on ${on_string}: results.tsv" from_work_dir="output_dir/results.tsv"/>
-  <data format="tabular" name="results_filtered_tsv" label="${tool.name} on ${on_string}: results.filtered.tsv" from_work_dir="output_dir/results.filtered.tsv"/>
-  <data format="tabular" name="results_classify_tsv" label="${tool.name} on ${on_string}: results.classify.tsv" from_work_dir="output_dir/results.classify.tsv"/>
+  <data format="txt" name="defuse_log" label="${tool.name} on ${on_string}: defuse.log" />
+  <data format="html" name="defuse_out" label="${tool.name} on ${on_string}: defuse_output">
+    <filter>keep_output == True</filter>
+  </data>
+  <data format="html" name="fusion_reads" label="${tool.name} on ${on_string}: fusion_reads">
+    <filter>do_get_reads == True</filter>
+  </data>
+  <data format="tabular" name="results_tsv" label="${tool.name} on ${on_string}: results.tsv" />
+  <data format="tabular" name="results_filtered_tsv" label="${tool.name} on ${on_string}: results.filtered.tsv" />
+  <data format="tabular" name="results_classify_tsv" label="${tool.name} on ${on_string}: results.classify.tsv" />
  </outputs>
  <tests>
  </tests>