comparison miRPlant.xml @ 44:0c4e11018934 draft

Uploaded

43:4c0b1a94b882

  <description>tool for plant microRNA analisis</description>

  <requirements>
    <requirement type="set_environment">SCRIPT_PATH</requirement>
    <requirement type="package" version="0.12.7">bowtie</requirement>
    <requirement type="package" version="2.11.0">R</requirement>
	<requirement type="package" version="0.0.13">fastx_toolkit </requirement>
	<requirement type="package" version="1.5.0">X11</requirement>
	<requirement type="package" version="2.1.8">ViennaRNA</requirement>
  </requirements>

  <!--command interpreter="perl">miPlant.pl -i $input -format $format -gfa $gfa -idx $index -pre $pre -mat $mat -rfam $rfam -idx2 $idx2 -D $D -a $a -M $M -min $min -max $max -mis $mis -e $e -f $f -v $v -r $r -dis $dis -flank $flank -mfe $mfe -t $t -o $output</command-->

    ##rank_of_series=$j
    -i ${s.input}
    -tag ${s.tag}
    #end for

    -format $format -gfa $gfa -pre $pre -mat $mat -rfam $rfam  -a $a -M $mapnt -min $min -max $max -mis $mismatch -e $e -f $f -v $v -r $r -dis $dis -flank $flank -mfe $mfe
  </command>

  <inputs>

   <repeat name="series" title="Series">

	<param name="flank" type="integer" value="10" label="Flank sequence length of miRNA precursor" />
	<param name="mfe" type="float" value="-30" label="Maximal free energy allowed for a miRNA precursor" />
  </inputs>

  <outputs>
   <data format="txt" name="known microRNA express list" from_work_dir="miRPlant_out/known_microRNA_express.txt"/>
   <data format="txt" name="known microRNA express alignment" from_work_dir="miRPlant_out/known_microRNA_express.aln"/>
   <data format="txt" name="known microRNA moRs result" from_work_dir="miRPlant_out/known_microRNA_express.moRs"/>
   <data format="txt" name="known microRNA precursor file" from_work_dir="miRPlant_out/known_microRNA_precursor.fa"/>
   <data format="txt" name="known microRNA mature file" from_work_dir="miRPlant_out/known_microRNA_mature.fa"/>
   <data format="txt" name="novel microRNA prediction file" from_work_dir="miRPlant_out/known_microRNA_mature.fa"/>
   <data format="txt" name="novel microRNA express list" from_work_dir="miRPlant_out/novel_microRNA_express.txt"/>
   <data format="txt" name="novel microRNA precursor file" from_work_dir="miRPlant_out/novel_microRNA_precursor.fa"/>
   <data format="txt" name="novel microRNA mature sequence file" from_work_dir="miRPlant_out/novel_microRNA_mature.fa"/>
   <data format="txt" name="analysis result" from_work_dir="miRPlant_out/result.html"/>
  </outputs>

 <help>

 </help>

44:0c4e11018934

  <description>tool for plant microRNA analisis</description>

  <requirements>
    <requirement type="set_environment">SCRIPT_PATH</requirement>
    <requirement type="package" version="0.12.7">bowtie</requirement>
    <requirement type="package" version="3.0.1">R</requirement>
	<requirement type="package" version="0.0.13">fastx_toolkit </requirement>
	<requirement type="package" version="1.5.0">libx11</requirement>
	<requirement type="package" version="2.1.8">ViennaRNA</requirement>
  </requirements>

  <!--command interpreter="perl">miPlant.pl -i $input -format $format -gfa $gfa -idx $index -pre $pre -mat $mat -rfam $rfam -idx2 $idx2 -D $D -a $a -M $M -min $min -max $max -mis $mis -e $e -f $f -v $v -r $r -dis $dis -flank $flank -mfe $mfe -t $t -o $output</command-->

    ##rank_of_series=$j
    -i ${s.input}
    -tag ${s.tag}
    #end for

    -format $format -gfa $gfa -pre $pre -mat $mat -rfam $rfam  -a $a -M $mapnt -min $min -max $max -mis $mismatch -e $e -f $f -v $v -r $r -dis $dis -flank $flank -mfe $mfe > run.log
  </command>

  <inputs>

   <repeat name="series" title="Series">

	<param name="flank" type="integer" value="10" label="Flank sequence length of miRNA precursor" />
	<param name="mfe" type="float" value="-30" label="Maximal free energy allowed for a miRNA precursor" />
  </inputs>

  <outputs>
   <data format="txt" name="known microRNA express list" from_work_dir="miRPlant_out/known_microRNA_express.txt" label="${tool.name} on ${on_string}: known microRNA express list"/>
   <data format="txt" name="known microRNA express alignment" from_work_dir="miRPlant_out/known_microRNA_express.aln" label="${tool.name} on ${on_string}: known microRNA express alignment"/>
   <data format="txt" name="known microRNA moRs result" from_work_dir="miRPlant_out/known_microRNA_express.moRs" label="${tool.name} on ${on_string}: known microRNA moRs result"/>
   <data format="txt" name="known microRNA precursor file" from_work_dir="miRPlant_out/known_microRNA_precursor.fa" label="${tool.name} on ${on_string}: known microRNA precursor file"/>
   <data format="txt" name="known microRNA mature file" from_work_dir="miRPlant_out/known_microRNA_mature.fa" label="${tool.name} on ${on_string}: known microRNA mature file"/>
   <data format="txt" name="novel microRNA express list" from_work_dir="miRPlant_out/novel_microRNA_express.txt" label="${tool.name} on ${on_string}: novel microRNA express list"/>
   <data format="txt" name="novel microRNA precursor file" from_work_dir="miRPlant_out/novel_microRNA_precursor.fa" label="${tool.name} on ${on_string}: novel microRNA precursor file"/>
   <data format="txt" name="novel microRNA mature sequence file" from_work_dir="miRPlant_out/novel_microRNA_mature.fa" label="${tool.name} on ${on_string}: novel microRNA mature sequence file"/>
   <data format="html" name="analysis result" from_work_dir="miRPlant_out/result.html" label="${tool.name} on ${on_string}: analysis result"/>
  </outputs>

 <help>

 </help>