Mercurial > repos > biomonika > linkyx
comparison LINKYX_identify_Y_linked_SNPs.xml @ 1:4c5de3a2c54e
toolshed2
| author | biomonika <biomonika@psu.edu> |
|---|---|
| date | Sun, 07 Sep 2014 23:12:26 -0400 |
| parents | 05c27700e5ca |
| children | 0d8315be76b7 |
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| 0:05c27700e5ca | 1:4c5de3a2c54e |
|---|---|
| 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</requirement> |
| 7 <requirement type="package" version="1.0.4">fastq_groomer</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> | |
| 7 </requirements> | 13 </requirements> |
| 8 <command interpreter="bash">LINKYX_identify_Y_linked_SNPs.sh $output $input1 $input2 $input3 $input4 $input5 $output1 $output2 $output3 $output4 $output5</command> | 14 <command interpreter="bash">LINKYX_identify_Y_linked_SNPs.sh $output $input1 $input2 $input3 $input4 $input5 $output1 $output2 $output3 $output4 $output5</command> |
| 9 <inputs> | 15 <inputs> |
| 10 <param format="fasta" name="input1" type="data" label="Reference"/> | 16 <param format="fasta" name="input1" type="data" label="Reference"/> |
| 11 <param format="bam" name="input2" type="data" label="Mother - Binary alignment format"/> | 17 <param format="bam" name="input2" type="data" label="Mother - Binary alignment format"/> |