Mercurial > repos > biomonika > linkyx
comparison LINKYX_identify_Y_linked_SNPs.xml @ 2:0d8315be76b7
Uploaded
| author | biomonika |
|---|---|
| date | Tue, 17 Feb 2015 21:59:51 -0500 |
| parents | 4c5de3a2c54e |
| children |
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| 1:4c5de3a2c54e | 2:0d8315be76b7 |
|---|---|
| 1 <tool id="LINKYX_Y" name="LINKYX_Y"> | 1 <tool id="LINKYX_Y" name="LINKYX_Y" version="1.1"> |
| 2 <description>Identify Y linked contigs from cross</description> | 2 <description>Identify Y linked contigs from cross</description> |
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="set_environment">LINKYX_PATH</requirement> | 4 <requirement type="set_environment">LINKYX_PATH</requirement> |
| 5 <requirement type="set_environment">SAMTOOLS</requirement> | 5 <requirement type="set_environment">SAMTOOLS</requirement> |
| 6 <requirement type="package" version="0.1.19">samtools</requirement> | 6 <requirement type="package" version="0.1.19">samtools-fpic</requirement> |
| 7 <requirement type="package" version="1.0.4">fastq_groomer</requirement> | 7 <requirement type="package" version="1.6.922">bioperl</requirement> |
| 8 <requirement type="package" version="0.0.1">trinityrnaseq</requirement> | |
| 9 <requirement type="package" version="1.2.3">bwa_wrappers</requirement> | |
| 10 <requirement type="package" version="1.1.4">sam_to_bam</requirement> | |
| 11 <requirement type="package" version="1.0.2">samtools_sort</requirement> | |
| 12 <requirement type="package" version="1.56.0">picard</requirement> | |
| 13 </requirements> | 8 </requirements> |
| 14 <command interpreter="bash">LINKYX_identify_Y_linked_SNPs.sh $output $input1 $input2 $input3 $input4 $input5 $output1 $output2 $output3 $output4 $output5</command> | 9 <command interpreter="bash">LINKYX_identify_Y_linked_SNPs.sh $output $input1 $input2 $input3 $input4 $input5 $output1 $output2 $output3 $output4 $output5</command> |
| 15 <inputs> | 10 <inputs> |
| 16 <param format="fasta" name="input1" type="data" label="Reference"/> | 11 <param format="fasta" name="input1" type="data" label="Reference"/> |
| 17 <param format="bam" name="input2" type="data" label="Mother - Binary alignment format"/> | 12 <param format="bam" name="input2" type="data" label="Mother - Binary alignment format"/> |