Mercurial > repos > big-tiandm > mirplant2
comparison miRPlant.xml @ 40:6a273db77b9b draft
Uploaded
| author | big-tiandm |
|---|---|
| date | Tue, 28 Oct 2014 01:33:03 -0400 |
| parents | 45d9b0f6a0d6 |
| children | 0c4e11018934 |
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| 39:2a5b751228a6 | 40:6a273db77b9b |
|---|---|
| 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="2.11.0">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="2.1.7">ViennaRNA</requirement> | 9 <requirement type="package" version="1.5.0">X11</requirement> |
| 10 <requirement type="package" version="2.1.8">ViennaRNA</requirement> | |
| 10 </requirements> | 11 </requirements> |
| 11 | 12 |
| 12 <!--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--> |
| 13 | 14 |
| 14 <command interpreter="perl">miRPlant.pl | 15 <command interpreter="perl">miRPlant.pl |
| 66 <param name="v" type="integer" value="0" label="report end-to-end hits less than v mismatches"/> | 67 <param name="v" type="integer" value="0" label="report end-to-end hits less than v mismatches"/> |
| 67 <param name="r" type="integer" value="25" label="a read is allowed to map up to this number of positions in the genome" /> | 68 <param name="r" type="integer" value="25" label="a read is allowed to map up to this number of positions in the genome" /> |
| 68 <param name="dis" type="integer" value="200" label="Maximal space between miRNA and miRNA*" /> | 69 <param name="dis" type="integer" value="200" label="Maximal space between miRNA and miRNA*" /> |
| 69 <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" /> |
| 70 <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" /> |
| 71 <param name="thread" type="integer" value="1" label="number of threads" /> | |
| 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"/> |
| 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"/> |