comparison defuse.xml @ 3:c90022a13c7c

DeFuse - Allow user to save the workspace, create an html file with links to the files in the workspace. Allow the creatation of an HTML formatted results.filtered.tsv with links to cluster detail provided by the get_read.pl command.

2:4245c2b047de

<tool id="defuse" name="DeFuse" version="1.1">
 <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>
 <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"/>
  <conditional name="refGenomeSource">
      <param name="genomeSource" type="select" label="Will you select a built-in DeFuse Reference Dataset, or supply a configuration from your history" help="">

      </when>
      <when value="history">
        <param name="config" type="data" format="txt" label="Defuse Config file" help=""/>
      </when>  <!-- history -->
  </conditional>  <!-- refGenomeSource -->
 </inputs>
 <configfiles>
  <configfile name="defuse_config">
#import ast
#if $refGenomeSource.genomeSource == "history":

# Bowtie parameters
bowtie_threads = #slurp
#try
$ref_dict['bowtie_threads']
#except
1
#end try
bowtie_quals = #slurp
#try
$ref_dict['bowtie_quals']
#except

#end raw

#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"/>
 </outputs>
 <tests>
 </tests>
 <help>
**DeFuse**

3:c90022a13c7c

<tool id="defuse" name="DeFuse" version="1.2">
 <description>identify fusion transcripts</description>
 <requirements>
  <requirement type="binary"></requirement>
 </requirements>
  <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"/>
  <conditional name="refGenomeSource">
      <param name="genomeSource" type="select" label="Will you select a built-in DeFuse Reference Dataset, or supply a configuration from your history" help="">

      </when>
      <when value="history">
        <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">
#import ast
#if $refGenomeSource.genomeSource == "history":

# Bowtie parameters
bowtie_threads = #slurp
#try
$ref_dict['bowtie_threads']
#except
4
#end try
bowtie_quals = #slurp
#try
$ref_dict['bowtie_quals']
#except

#end raw

#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 ${on_string}: defuse.log" />
  <data format="html" name="defuse_out" label="${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>
 <help>
**DeFuse**