Mercurial > repos > biomonika > linkyx

annotate LINKYX_identify_X_linked_SNPs.xml @ 2:0d8315be76b7

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author biomonika
date Tue, 17 Feb 2015 21:59:51 -0500
parents 4c5de3a2c54e
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
0d8315be76b7 Uploaded
biomonika
parents: 1
diff changeset
1 <tool id="LINKYX_X" name="LINKYX_X" version="1.1">
0
05c27700e5ca initial commit
biomonika <biomonika@psu.edu>
parents:
diff changeset
2 <description>Identify X linked contigs from cross</description>
05c27700e5ca initial commit
biomonika <biomonika@psu.edu>
parents:
diff changeset
3 <requirements>
05c27700e5ca initial commit
biomonika <biomonika@psu.edu>
parents:
diff changeset
4 <requirement type="set_environment">LINKYX_PATH</requirement>
05c27700e5ca initial commit
biomonika <biomonika@psu.edu>
parents:
diff changeset
5 <requirement type="set_environment">SAMTOOLS</requirement>
2
0d8315be76b7 Uploaded
biomonika
parents: 1
diff changeset
6 <requirement type="package" version="0.1.19">samtools-fpic</requirement>
0d8315be76b7 Uploaded
biomonika
parents: 1
diff changeset
7 <requirement type="package" version="1.6.922">bioperl</requirement>
0
05c27700e5ca initial commit
biomonika <biomonika@psu.edu>
parents:
diff changeset
8 </requirements>
05c27700e5ca initial commit
biomonika <biomonika@psu.edu>
parents:
diff changeset
9 <command interpreter="bash">LINKYX_identify_X_linked_SNPs.sh $output $input1 $input2 $input3 $input4 $input5 $input6 $input7 $input8 $input9 $output1 $output2 $output3 $output4 $output5</command>
05c27700e5ca initial commit
biomonika <biomonika@psu.edu>
parents:
diff changeset
10 <inputs>
05c27700e5ca initial commit
biomonika <biomonika@psu.edu>
parents:
diff changeset
11 <param format="fasta" name="input1" type="data" label="Reference"/>
05c27700e5ca initial commit
biomonika <biomonika@psu.edu>
parents:
diff changeset
12 <param format="bam" name="input2" type="data" label="Mother - Binary alignment format"/>
05c27700e5ca initial commit
biomonika <biomonika@psu.edu>
parents:
diff changeset
13 <param format="vcf" name="input3" type="data" label="Mother - Variant call format"/>
05c27700e5ca initial commit
biomonika <biomonika@psu.edu>
parents:
diff changeset
14 <param format="bam" name="input4" type="data" label="Father - Binary alignment format"/>
05c27700e5ca initial commit
biomonika <biomonika@psu.edu>
parents:
diff changeset
15 <param format="vcf" name="input5" type="data" label="Father - Variant call format"/>
05c27700e5ca initial commit
biomonika <biomonika@psu.edu>
parents:
diff changeset
16 <param format="bam" name="input6" type="data" label="Daughter - Binary alignment format"/>
05c27700e5ca initial commit
biomonika <biomonika@psu.edu>
parents:
diff changeset
17 <param format="vcf" name="input7" type="data" label="Daughter - Variant call format"/>
05c27700e5ca initial commit
biomonika <biomonika@psu.edu>
parents:
diff changeset
18 <param format="bam" name="input8" type="data" label="Son - Binary alignment format"/>
05c27700e5ca initial commit
biomonika <biomonika@psu.edu>
parents:
diff changeset
19 <param format="vcf" name="input9" type="data" label="Son - Variant call format"/>
05c27700e5ca initial commit
biomonika <biomonika@psu.edu>
parents:
diff changeset
20 </inputs>
05c27700e5ca initial commit
biomonika <biomonika@psu.edu>
parents:
diff changeset
21 <outputs>
05c27700e5ca initial commit
biomonika <biomonika@psu.edu>
parents:
diff changeset
22 <data format="txt" name="output" />
05c27700e5ca initial commit
biomonika <biomonika@psu.edu>
parents:
diff changeset
23 <data format="fasta" name="output1" label="X_sequences.fasta " />
05c27700e5ca initial commit
biomonika <biomonika@psu.edu>
parents:
diff changeset
24 <data format="bam" name="output2" label="Mother bam file - X linked " />
05c27700e5ca initial commit
biomonika <biomonika@psu.edu>
parents:
diff changeset
25 <data format="bam" name="output3" label="Father bam file - X linked " />
05c27700e5ca initial commit
biomonika <biomonika@psu.edu>
parents:
diff changeset
26 <data format="bam" name="output4" label="Daughter bam file - X linked " />
05c27700e5ca initial commit
biomonika <biomonika@psu.edu>
parents:
diff changeset
27 <data format="bam" name="output5" label="Son bam file - X linked " />
05c27700e5ca initial commit
biomonika <biomonika@psu.edu>
parents:
diff changeset
28 </outputs>
05c27700e5ca initial commit
biomonika <biomonika@psu.edu>
parents:
diff changeset
29
05c27700e5ca initial commit
biomonika <biomonika@psu.edu>
parents:
diff changeset
30 <tests>
05c27700e5ca initial commit
biomonika <biomonika@psu.edu>
parents:
diff changeset
31 <test>
05c27700e5ca initial commit
biomonika <biomonika@psu.edu>
parents:
diff changeset
32 <output name="out_file1" file="X_results.txt"/>
05c27700e5ca initial commit
biomonika <biomonika@psu.edu>
parents:
diff changeset
33 </test>
05c27700e5ca initial commit
biomonika <biomonika@psu.edu>
parents:
diff changeset
34 </tests>
05c27700e5ca initial commit
biomonika <biomonika@psu.edu>
parents:
diff changeset
35
05c27700e5ca initial commit
biomonika <biomonika@psu.edu>
parents:
diff changeset
36 <help>
05c27700e5ca initial commit
biomonika <biomonika@psu.edu>
parents:
diff changeset
37 This tool identifies X linked contigs from cross (represented as 4 VCF files).
05c27700e5ca initial commit
biomonika <biomonika@psu.edu>
parents:
diff changeset
38 </help>
05c27700e5ca initial commit
biomonika <biomonika@psu.edu>
parents:
diff changeset
39
2
0d8315be76b7 Uploaded
biomonika
parents: 1
diff changeset
40 </tool>