comparison datamanager_create_reference.xml @ 45:aedaa66483f1 draft

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44:225750bf3770

<tool id="data_manager_defuse_reference" name="DeFuse Reference DataManager" version="1.6.1" tool_type="manage_data">
 <description>create a defuse reference from Ensembl and UCSC sources</description>
 <requirements>
  <requirement type="package" version="0.6.1">defuse</requirement>
  <requirement type="package" version="0.1.18">samtools</requirement>
  <requirement type="package" version="1.0.0">bowtie</requirement>
  <requirement type="package" version="2013-05-09">gmap</requirement>
  <requirement type="package" version="latest">kent</requirement>
 </requirements>
 <command interpreter="python"> datamanager_create_reference.py 
    --dbkey $genome.ensembl_genome_version 
    --description "$genome.ensembl_prefix $genome.ensembl_genome_version ($genome.ucsc_genome_version)"
    --defuse_config $defuse_config
    --defuse_script $defuse_script
    $out_file
 </command>
 <inputs>
  <conditional name="genome">
    <param name="choice" type="select" label="Select a Genome Build">
      <option value="GRCh38">Homo_sapiens GRCh38  hg38</option>
      <option value="GRCh37">Homo_sapiens GRCh37  hg19</option>

bowtie_build_bin = __BOWTIE_BUILD_BIN__
blat_bin = __BLAT_BIN__
fatotwobit_bin = __FATOTWOBIT_BIN__
gmap_bin = __GMAP_BIN__
gmap_setup_bin = __GMAP_SETUP_BIN__
r_bin = __R_BIN__
rscript_bin = __RSCRIPT_BIN__

#raw
# Directory where you want your dataset

# Remove temp files
remove_job_files                            = yes
remove_job_temp_files                       = yes
#end raw
  </configfile>
  <configfile name="defuse_script">#slurp
#!/bin/bash
## define some things for cheetah proccessing
#set $amp = chr(38)
#set $gt = chr(62)
## substitute pathnames into config file
if `grep __DATASET_DIRECTORY__ $defuse_config ${gt} /dev/null`;then sed -i'.tmp' "s#__DATASET_DIRECTORY__#\$1#" $defuse_config; fi
if `grep __DEFUSE_PATH__ $defuse_config ${gt} /dev/null`;then sed -i'.tmp' "s#__DEFUSE_PATH__#\${DEFUSE_PATH}#" $defuse_config; fi
if `grep __SAMTOOLS_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} SAMTOOLS_BIN=`which samtools`;then sed -i'.tmp' "s#__SAMTOOLS_BIN__#\${SAMTOOLS_BIN}#" $defuse_config; fi
if `grep __BOWTIE_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} BOWTIE_BIN=`which bowtie`;then sed -i'.tmp' "s#__BOWTIE_BIN__#\${BOWTIE_BIN}#" $defuse_config; fi
if `grep __BOWTIE_BUILD_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} BOWTIE_BUILD_BIN=`which bowtie-build`;then sed -i'.tmp' "s#__BOWTIE_BUILD_BIN__#\${BOWTIE_BUILD_BIN}#" $defuse_config; fi
if `grep __BLAT_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} BLAT_BIN=`which blat`;then sed -i'.tmp' "s#__BLAT_BIN__#\${BLAT_BIN}#" $defuse_config; fi
if `grep __FATOTWOBIT_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} FATOTWOBIT_BIN=`which faToTwoBit`;then sed -i'.tmp' "s#__FATOTWOBIT_BIN__#\${FATOTWOBIT_BIN}#" $defuse_config; fi
if `grep __GMAP_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} GMAP_BIN=`which gmap`;then sed -i'.tmp' "s#__GMAP_BIN__#\${GMAP_BIN}#" $defuse_config; fi
if `grep __GMAP_SETUP_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} GMAP_SETUP_BIN=`which gmap_setup`;then sed -i'.tmp' "s#__GMAP_SETUP_BIN__#\${GMAP_SETUP_BIN}#" $defuse_config; fi
if `grep __GMAP_INDEX_DIR__ $defuse_config ${gt} /dev/null` ${amp}${amp} GMAP_INDEX_DIR=`pwd`/gmap;then sed -i'.tmp' "s#__GMAP_INDEX_DIR__#\${GMAP_INDEX_DIR}#" $defuse_config; fi
if `grep __R_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} R_BIN=`which R`;then sed -i'.tmp' "s#__R_BIN__#\${R_BIN}#" $defuse_config; fi
if `grep __RSCRIPT_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} RSCRIPT_BIN=`which Rscript`;then sed -i'.tmp' "s#__RSCRIPT_BIN__#\${RSCRIPT_BIN}#" $defuse_config; fi
## copy config to output
cp $defuse_config \$1/defuse_config.txt
## Run the create_reference_dataset.pl
perl \${DEFUSE_PATH}/scripts/create_reference_dataset.pl -c $defuse_config 
  </configfile>
 </configfiles>

 <tests>
 </tests>
 <help>

45:aedaa66483f1

<tool id="data_manager_defuse_reference" name="DeFuse Reference DataManager" version="@DEFUSE_VERSION@.1" tool_type="manage_data">
 <description>create a defuse reference from Ensembl and UCSC sources</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>
        <expand macro="defuse_requirement" />
    </requirements>
    <command interpreter="python"><![CDATA[
        datamanager_create_reference.py 
        --dbkey $genome.ensembl_genome_version 
        --description "$genome.ensembl_prefix $genome.ensembl_genome_version ($genome.ucsc_genome_version)"
        --defuse_config $defuse_config
        --defuse_script $defuse_script
        $out_file
    ]]></command>
 <inputs>
  <conditional name="genome">
    <param name="choice" type="select" label="Select a Genome Build">
      <option value="GRCh38">Homo_sapiens GRCh38  hg38</option>
      <option value="GRCh37">Homo_sapiens GRCh37  hg19</option>

bowtie_build_bin = __BOWTIE_BUILD_BIN__
blat_bin = __BLAT_BIN__
fatotwobit_bin = __FATOTWOBIT_BIN__
gmap_bin = __GMAP_BIN__
gmap_setup_bin = __GMAP_SETUP_BIN__
gmap_build_bin = __GMAP_BUILD_BIN__
r_bin = __R_BIN__
rscript_bin = __RSCRIPT_BIN__

#raw
# Directory where you want your dataset

# Remove temp files
remove_job_files                            = yes
remove_job_temp_files                       = yes
#end raw
  </configfile>
  <configfile name="defuse_script"><![CDATA[#slurp
#!/bin/bash
## define some things for cheetah proccessing
#set $gt = chr(62)
## substitute pathnames into config file
export DATASET_DIRECTORY=$1
if `grep __DATASET_DIRECTORY__ $defuse_config > /dev/null`;then sed -i'.tmp' "s#__DATASET_DIRECTORY__#\$DATASET_DIRECTORY#" $defuse_config; fi
if `grep __DEFUSE_PATH__ $defuse_config > /dev/null`;then sed -i'.tmp' "s#__DEFUSE_PATH__#\${DEFUSE_PATH}#" $defuse_config; fi
if `grep __SAMTOOLS_BIN__ $defuse_config > /dev/null` && SAMTOOLS_BIN=`which samtools`;then sed -i'.tmp' "s#__SAMTOOLS_BIN__#\${SAMTOOLS_BIN}#" $defuse_config; fi
if `grep __BOWTIE_BIN__ $defuse_config > /dev/null` && BOWTIE_BIN=`which bowtie`;then sed -i'.tmp' "s#__BOWTIE_BIN__#\${BOWTIE_BIN}#" $defuse_config; fi
if `grep __BOWTIE_BUILD_BIN__ $defuse_config > /dev/null` && BOWTIE_BUILD_BIN=`which bowtie-build`;then sed -i'.tmp' "s#__BOWTIE_BUILD_BIN__#\${BOWTIE_BUILD_BIN}#" $defuse_config; fi
if `grep __BLAT_BIN__ $defuse_config > /dev/null` && BLAT_BIN=`which blat`;then sed -i'.tmp' "s#__BLAT_BIN__#\${BLAT_BIN}#" $defuse_config; fi
if `grep __FATOTWOBIT_BIN__ $defuse_config > /dev/null` && FATOTWOBIT_BIN=`which faToTwoBit`;then sed -i'.tmp' "s#__FATOTWOBIT_BIN__#\${FATOTWOBIT_BIN}#" $defuse_config; fi
if `grep __GMAP_BIN__ $defuse_config > /dev/null` && GMAP_BIN=`which gmap`;then sed -i'.tmp' "s#__GMAP_BIN__#\${GMAP_BIN}#" $defuse_config; fi
if `grep __GMAP_BUILD_BIN__ $defuse_config > /dev/null` && GMAP_BUILD_BIN=`which gmap_setup`;then sed -i'.tmp' "s#__GMAP_BUILD_BIN__#\${GMAP_BUILD_BIN}#" $defuse_config; fi
if `grep __GMAP_INDEX_DIR__ $defuse_config > /dev/null` && GMAP_INDEX_DIR=`pwd`/gmap;then sed -i'.tmp' "s#__GMAP_INDEX_DIR__#\${GMAP_INDEX_DIR}#" $defuse_config; fi
if `grep __R_BIN__ $defuse_config > /dev/null` && R_BIN=`which R`;then sed -i'.tmp' "s#__R_BIN__#\${R_BIN}#" $defuse_config; fi
if `grep __RSCRIPT_BIN__ $defuse_config > /dev/null` && RSCRIPT_BIN=`which Rscript`;then sed -i'.tmp' "s#__RSCRIPT_BIN__#\${RSCRIPT_BIN}#" $defuse_config; fi
## copy config to output
cp $defuse_config \$1/defuse_config.txt
## Run defuse_create_ref.pl
defuse_create_ref.pl --config $defuse_config --dataset $DATASET_DIRECTORY
  ]]></configfile>
 </configfiles>

 <tests>
 </tests>
 <help>