Mercurial > repos > galaxyp > psm_to_sam

annotate tool-data/customProDB.loc.sample @ 5:7d02e2e2c8fa draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
author galaxyp
date Thu, 28 Jan 2016 18:46:22 -0500
parents
children cd69250e1150
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5
7d02e2e2c8fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
1 #This file lists the locations and dbkeys of all the fasta files
7d02e2e2c8fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
2 #under the "genome" directory (a directory that contains a directory
7d02e2e2c8fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
3 #for each build). The script extract_fasta.py will generate the file
7d02e2e2c8fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
4 #all_fasta.loc. This file has the format (white space characters are
7d02e2e2c8fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
5 #TAB characters):
7d02e2e2c8fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
6 #
7d02e2e2c8fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
7 #<unique_build_id> <dbkey> <display_name> <file_path>
7d02e2e2c8fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
8 #
7d02e2e2c8fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
9 #So, all_fasta.loc could look something like this:
7d02e2e2c8fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
10 #
7d02e2e2c8fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
11 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
7d02e2e2c8fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
12 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
7d02e2e2c8fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
13 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
7d02e2e2c8fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
14 #
7d02e2e2c8fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
15 #Your all_fasta.loc file should contain an entry for each individual
7d02e2e2c8fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
16 #fasta file. So there will be multiple fasta files for each build,
7d02e2e2c8fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
17 #such as with hg19 above.
7d02e2e2c8fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
18 #