Mercurial > repos > big-tiandm > mirplant2

comparison miRPlant.xml @ 44:0c4e11018934 draft

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author big-tiandm
date Thu, 30 Oct 2014 21:29:19 -0400
parents 6a273db77b9b
children ca05d68aca13
comparison
equal deleted inserted replaced
43:4c0b1a94b882 44:0c4e11018934
2 <description>tool for plant microRNA analisis</description> 2 <description>tool for plant microRNA analisis</description>
3 3
4 <requirements> 4 <requirements>
5 <requirement type="set_environment">SCRIPT_PATH</requirement> 5 <requirement type="set_environment">SCRIPT_PATH</requirement>
6 <requirement type="package" version="0.12.7">bowtie</requirement> 6 <requirement type="package" version="0.12.7">bowtie</requirement>
7 <requirement type="package" version="2.11.0">R</requirement> 7 <requirement type="package" version="3.0.1">R</requirement>
8 <requirement type="package" version="0.0.13">fastx_toolkit </requirement> 8 <requirement type="package" version="0.0.13">fastx_toolkit </requirement>
9 <requirement type="package" version="1.5.0">X11</requirement> 9 <requirement type="package" version="1.5.0">libx11</requirement>
10 <requirement type="package" version="2.1.8">ViennaRNA</requirement> 10 <requirement type="package" version="2.1.8">ViennaRNA</requirement>
11 </requirements> 11 </requirements>
12 12
13 <!--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--> 13 <!--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 $output</command-->
14 14
25 ##rank_of_series=$j 25 ##rank_of_series=$j
26 -i ${s.input} 26 -i ${s.input}
27 -tag ${s.tag} 27 -tag ${s.tag}
28 #end for 28 #end for
29 29
30 -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 30 -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 $mfe > run.log
31 </command> 31 </command>
32 32
33 <inputs> 33 <inputs>
34 34
35 <repeat name="series" title="Series"> 35 <repeat name="series" title="Series">
70 <param name="flank" type="integer" value="10" label="Flank sequence length of miRNA precursor" /> 70 <param name="flank" type="integer" value="10" label="Flank sequence length of miRNA precursor" />
71 <param name="mfe" type="float" value="-30" label="Maximal free energy allowed for a miRNA precursor" /> 71 <param name="mfe" type="float" value="-30" label="Maximal free energy allowed for a miRNA precursor" />
72 </inputs> 72 </inputs>
73 73
74 <outputs> 74 <outputs>
75 <data format="txt" name="known microRNA express list" from_work_dir="miRPlant_out/known_microRNA_express.txt"/> 75 <data format="txt" name="known microRNA express list" from_work_dir="miRPlant_out/known_microRNA_express.txt" label="${tool.name} on ${on_string}: known microRNA express list"/>
76 <data format="txt" name="known microRNA express alignment" from_work_dir="miRPlant_out/known_microRNA_express.aln"/> 76 <data format="txt" name="known microRNA express alignment" from_work_dir="miRPlant_out/known_microRNA_express.aln" label="${tool.name} on ${on_string}: known microRNA express alignment"/>
77 <data format="txt" name="known microRNA moRs result" from_work_dir="miRPlant_out/known_microRNA_express.moRs"/> 77 <data format="txt" name="known microRNA moRs result" from_work_dir="miRPlant_out/known_microRNA_express.moRs" label="${tool.name} on ${on_string}: known microRNA moRs result"/>
78 <data format="txt" name="known microRNA precursor file" from_work_dir="miRPlant_out/known_microRNA_precursor.fa"/> 78 <data format="txt" name="known microRNA precursor file" from_work_dir="miRPlant_out/known_microRNA_precursor.fa" label="${tool.name} on ${on_string}: known microRNA precursor file"/>
79 <data format="txt" name="known microRNA mature file" from_work_dir="miRPlant_out/known_microRNA_mature.fa"/> 79 <data format="txt" name="known microRNA mature file" from_work_dir="miRPlant_out/known_microRNA_mature.fa" label="${tool.name} on ${on_string}: known microRNA mature file"/>
80 <data format="txt" name="novel microRNA prediction file" from_work_dir="miRPlant_out/known_microRNA_mature.fa"/> 80 <data format="txt" name="novel microRNA express list" from_work_dir="miRPlant_out/novel_microRNA_express.txt" label="${tool.name} on ${on_string}: novel microRNA express list"/>
81 <data format="txt" name="novel microRNA express list" from_work_dir="miRPlant_out/novel_microRNA_express.txt"/> 81 <data format="txt" name="novel microRNA precursor file" from_work_dir="miRPlant_out/novel_microRNA_precursor.fa" label="${tool.name} on ${on_string}: novel microRNA precursor file"/>
82 <data format="txt" name="novel microRNA precursor file" from_work_dir="miRPlant_out/novel_microRNA_precursor.fa"/> 82 <data format="txt" name="novel microRNA mature sequence file" from_work_dir="miRPlant_out/novel_microRNA_mature.fa" label="${tool.name} on ${on_string}: novel microRNA mature sequence file"/>
83 <data format="txt" name="novel microRNA mature sequence file" from_work_dir="miRPlant_out/novel_microRNA_mature.fa"/> 83 <data format="html" name="analysis result" from_work_dir="miRPlant_out/result.html" label="${tool.name} on ${on_string}: analysis result"/>
84 <data format="txt" name="analysis result" from_work_dir="miRPlant_out/result.html"/>
85 </outputs> 84 </outputs>
86 85
87 <help> 86 <help>
88 87
89 </help> 88 </help>