Mercurial > repos > galaxyp > psm_to_sam
comparison PSM2SAM.R @ 2:757ecf27b4a9 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 969036a4673f5565185badb0d4fe513a7b784261
author | galaxyp |
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date | Mon, 25 Sep 2017 13:23:54 -0400 |
parents | 90ecb65017a0 |
children | 16c4cc7793e9 |
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1:3192cb6a88f6 | 2:757ecf27b4a9 |
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51 { | 51 { |
52 stop("failed to read header lines from bam_file") | 52 stop("failed to read header lines from bam_file") |
53 } | 53 } |
54 | 54 |
55 # load customProDB from GitHub (NOTE: downloading the zip is faster than cloning the repo with git2r or devtools::install_github) | 55 # load customProDB from GitHub (NOTE: downloading the zip is faster than cloning the repo with git2r or devtools::install_github) |
56 download.file("https://github.com/chambm/customProDB/archive/master.zip", "customProDB.zip", quiet=TRUE) | 56 download.file("https://github.com/chambm/customProDB/archive/c57e5498392197bc598a18c26acb70d7530a921c.zip", "customProDB.zip", quiet=TRUE) |
57 unzip("customProDB.zip") | 57 unzip("customProDB.zip") |
58 devtools::load_all("customProDB-master") | 58 devtools::load_all("customProDB-c57e5498392197bc598a18c26acb70d7530a921c") |
59 | 59 |
60 # load proBAMr from GitHub | 60 # load proBAMr from GitHub |
61 download.file("https://github.com/chambm/proBAMr/archive/master.zip", "proBAMr.zip", quiet=TRUE) | 61 download.file("https://github.com/chambm/proBAMr/archive/a03edf68f51215be40717c5374f39ce67bd2e68b.zip", "proBAMr.zip", quiet=TRUE) |
62 unzip("proBAMr.zip") | 62 unzip("proBAMr.zip") |
63 devtools::load_all("proBAMr-master") | 63 devtools::load_all("proBAMr-a03edf68f51215be40717c5374f39ce67bd2e68b") |
64 | 64 |
65 psmInputLength = length(idpDB_file)+length(pepXmlTab_file)+length(peptideShakerPsmReport_file) | 65 psmInputLength = length(idpDB_file)+length(pepXmlTab_file)+length(peptideShakerPsmReport_file) |
66 if (psmInputLength == 0) | 66 if (psmInputLength == 0) |
67 { | 67 { |
68 stop("one of the input PSM file parameters must be specified") | 68 stop("one of the input PSM file parameters must be specified") |