Mercurial > repos > galaxyp > msgfplus
comparison msgfplus.xml @ 4:58f9cf0de6d4 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit b2712071afd2d74261bc3e3fc555355f5675a0d6
author | galaxyp |
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date | Wed, 23 Aug 2017 05:47:29 -0400 |
parents | b4ccaf21855d |
children | ce4882b95b73 |
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3:b4ccaf21855d | 4:58f9cf0de6d4 |
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1 <tool id="msgfplus" name="MS-GF+" version="0.1"> | 1 <tool id="msgfplus" name="MS-GF+" version="0.2"> |
2 <description> | 2 <description> |
3 Identifies peptides in tandem mass spectra using the MS-GF+ search engine. | 3 Identifies peptides in tandem mass spectra using the MS-GF+ search engine. |
4 </description> | 4 </description> |
5 <requirements> | 5 <requirements> |
6 <requirement type="package" version="2016.10.26">msgf_plus</requirement> | 6 <requirement type="package" version="2016.10.26">msgf_plus</requirement> |
12 </stdio> | 12 </stdio> |
13 <command> | 13 <command> |
14 | 14 |
15 <![CDATA[ | 15 <![CDATA[ |
16 #if $msgf_input.intype_selector == "single" | 16 #if $msgf_input.intype_selector == "single" |
17 #set $db_name = $msgf_input.d.display_name.replace(".fasta", "") + ".fasta" | 17 #set $db_name = $msgf_input.d.element_identifier.replace(".fasta", "") + ".fasta" |
18 #set $input_name = $msgf_input.s.display_name | 18 #set $input_name = $msgf_input.s.element_identifier.replace(".mzML", "") + ".mzML" |
19 ln -s '$msgf_input.s' '${input_name}' && | 19 ln -s '$msgf_input.s' '${input_name}' && |
20 ln -s '$msgf_input.d' '${db_name}' && | 20 ln -s '$msgf_input.d' '${db_name}' && |
21 #else if $msgf_input.intype_selector == "fractions" | 21 #else if $msgf_input.intype_selector == "fractions" |
22 #set $db_name = $msgf_input.db_spectra.reverse.display_name.replace(".fasta", "") + ".fasta" | 22 #set $db_name = $msgf_input.db_spectra.reverse.element_identifier.replace(".fasta", "") + ".fasta" |
23 #set $input_name = $msgf_input.db_spectra.forward.display_name | 23 #set $input_name = $msgf_input.db_spectra.forward.element_identifier.replace(".mzML", "") + ".mzML" |
24 ln -s '$msgf_input.db_spectra.forward' '${input_name}' && | 24 ln -s '$msgf_input.db_spectra.forward' '${input_name}' && |
25 ln -s '$msgf_input.db_spectra.reverse' '${db_name}' && | 25 ln -s '$msgf_input.db_spectra.reverse' '${db_name}' && |
26 #end if | 26 #end if |
27 #set $output_name = $input_name.replace(".mzML", "") + ".mzid" | 27 #set $output_name = $input_name.replace(".mzML", ".mzid") |
28 | 28 |
29 echo \\#Mods > Mods.txt && | 29 echo \\#Mods > Mods.txt && |
30 #set $common_mods = str($common_fixed_modifications) + "," + str($common_variable_modifications) | 30 #set $common_mods = str($common_fixed_modifications) + "," + str($common_variable_modifications) |
31 #for $mod in $common_mods.split(",") | 31 #for $mod in $common_mods.split(",") |
32 echo '$mod.replace("_", ",")' >> Mods.txt && | 32 echo '$mod.replace("_", ",")' >> Mods.txt && |
76 <param argument="-s" type="data" format="mzml" label="Input Raw MS File(s)"/> | 76 <param argument="-s" type="data" format="mzml" label="Input Raw MS File(s)"/> |
77 <param argument="-d" type="data" format="fasta" label="Protein Database" help="Select FASTA database from history"/> | 77 <param argument="-d" type="data" format="fasta" label="Protein Database" help="Select FASTA database from history"/> |
78 </when> | 78 </when> |
79 <when value="fractions"> | 79 <when value="fractions"> |
80 <param name="db_spectra" type="data_collection" collection_type="paired" | 80 <param name="db_spectra" type="data_collection" collection_type="paired" |
81 label="Collection: Pairs of FASTA database (forward) and spectra (reverse)"/> | 81 label="Collection: Pairs of spectra (forward) and FASTA database (reverse)"/> |
82 </when> | 82 </when> |
83 </conditional> | 83 </conditional> |
84 <param name="tsvcheck" type="boolean" label="Output TSV as well?" /> | 84 <param name="tsvcheck" type="boolean" label="Output TSV as well?" /> |
85 <param argument="-tda" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Search with on-the-fly decoy database?" help="MSGF+ uses XXX_ as an accession prefix to indicate a decoy hit" /> | 85 <param argument="-tda" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Search with on-the-fly decoy database?" help="MSGF+ uses XXX_ as an accession prefix to indicate a decoy hit" /> |
86 <param argument="-t" type="float" value="10" label="Precursor mass tolerance" help="Error tolerance for matching peptide mass to precursor ion mass"/> | 86 <param argument="-t" type="float" value="10" label="Precursor mass tolerance" help="Error tolerance for matching peptide mass to precursor ion mass"/> |
267 <param name="ntt" value="1" /> | 267 <param name="ntt" value="1" /> |
268 <param name="t" value="50" /> | 268 <param name="t" value="50" /> |
269 <param name="precursor_ion_tol_units" value="ppm" /> | 269 <param name="precursor_ion_tol_units" value="ppm" /> |
270 <param name="common_fixed_modifications" value="" /> | 270 <param name="common_fixed_modifications" value="" /> |
271 <param name="common_variable_modifications" value="" /> | 271 <param name="common_variable_modifications" value="" /> |
272 <output name="output" file="201208-378803-msgf_20161026-50ppm-semitryptic-no_mods.mzid" compare="sim_size" delta="20" /> | 272 <output name="output" file="201208-378803-msgf_20161026-50ppm-semitryptic-no_mods.mzid" compare="sim_size" delta="100" /> |
273 </test> | 273 </test> |
274 <test> | 274 <test> |
275 <param name="msgf_input|intype_selector" value="single" /> | 275 <param name="msgf_input|intype_selector" value="single" /> |
276 <param name="msgf_input|s" value="input/201208-378803.mzML" /> | 276 <param name="msgf_input|s" value="input/201208-378803.mzML" /> |
277 <param name="msgf_input|d" value="input/cow.protein.PRG2012-subset.fasta" /> | 277 <param name="msgf_input|d" value="input/cow.protein.PRG2012-subset.fasta" /> |