Mercurial > repos > galaxyp > msgfplus
annotate msgfplus.xml @ 8:47408c5b1517 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit a030bdf85b5d74b7c1a16926322e47154b120fea
| author | galaxyp |
|---|---|
| date | Wed, 13 Sep 2017 15:57:15 -0400 |
| parents | 51fd56b09e64 |
| children | b45ced785e01 |
| rev | line source |
|---|---|
|
8
47408c5b1517
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit a030bdf85b5d74b7c1a16926322e47154b120fea
galaxyp
parents:
7
diff
changeset
|
1 <tool id="msgfplus" name="MS-GF+" version="0.3"> |
|
0
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
2 <description> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
3 Identifies peptides in tandem mass spectra using the MS-GF+ search engine. |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
4 </description> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
5 <requirements> |
|
5
468e8d70a073
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
4
diff
changeset
|
6 <requirement type="package" version="2016.10.26">msgf_plus</requirement> |
|
0
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
7 </requirements> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
8 <stdio> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
9 <exit_code range="1:" level="fatal" description="Job Failed" /> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
10 <regex match="java.*Exception" level="fatal" description="Java Exception"/> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
11 <regex match="Could not create the Java virtual machine" level="fatal" description="JVM Error"/> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
12 </stdio> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
13 <command> |
|
5
468e8d70a073
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
4
diff
changeset
|
14 |
|
0
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
15 <![CDATA[ |
|
5
468e8d70a073
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
4
diff
changeset
|
16 #if $msgf_input.intype_selector == "single" |
|
7
51fd56b09e64
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit b2712071afd2d74261bc3e3fc555355f5675a0d6
galaxyp
parents:
6
diff
changeset
|
17 #set $db_name = $msgf_input.d.element_identifier.replace(".fasta", "") + ".fasta" |
|
51fd56b09e64
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit b2712071afd2d74261bc3e3fc555355f5675a0d6
galaxyp
parents:
6
diff
changeset
|
18 #set $input_name = $msgf_input.s.element_identifier.replace(".mzML", "") + ".mzML" |
|
5
468e8d70a073
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
4
diff
changeset
|
19 ln -s '$msgf_input.s' '${input_name}' && |
|
468e8d70a073
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
4
diff
changeset
|
20 ln -s '$msgf_input.d' '${db_name}' && |
|
468e8d70a073
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
4
diff
changeset
|
21 #else if $msgf_input.intype_selector == "fractions" |
|
7
51fd56b09e64
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit b2712071afd2d74261bc3e3fc555355f5675a0d6
galaxyp
parents:
6
diff
changeset
|
22 #set $db_name = $msgf_input.db_spectra.reverse.element_identifier.replace(".fasta", "") + ".fasta" |
|
8
47408c5b1517
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit a030bdf85b5d74b7c1a16926322e47154b120fea
galaxyp
parents:
7
diff
changeset
|
23 #set $input_name = $msgf_input.db_spectra.name.replace(".mzML", "") + ".mzML" |
|
5
468e8d70a073
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
4
diff
changeset
|
24 ln -s '$msgf_input.db_spectra.forward' '${input_name}' && |
|
468e8d70a073
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
4
diff
changeset
|
25 ln -s '$msgf_input.db_spectra.reverse' '${db_name}' && |
|
468e8d70a073
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
4
diff
changeset
|
26 #end if |
|
7
51fd56b09e64
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit b2712071afd2d74261bc3e3fc555355f5675a0d6
galaxyp
parents:
6
diff
changeset
|
27 #set $output_name = $input_name.replace(".mzML", ".mzid") |
|
0
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
28 |
|
1
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
29 echo \\#Mods > Mods.txt && |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
30 #set $common_mods = str($common_fixed_modifications) + "," + str($common_variable_modifications) |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
31 #for $mod in $common_mods.split(",") |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
32 echo '$mod.replace("_", ",")' >> Mods.txt && |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
33 #end for |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
34 |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
35 #for $mod in $custom_mods |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
36 echo '${mod.formula_or_mass},${mod.aa_specificity},${mod.fix_or_opt},${mod.position_specificity},${mod.mod_name}' >> Mods.txt && |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
37 #end for |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
38 |
|
5
468e8d70a073
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
4
diff
changeset
|
39 msgf_plus |
|
0
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
40 -s '$input_name' |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
41 -d '$db_name' |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
42 -thread \${GALAXY_SLOTS:-1} |
|
1
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
43 -mod Mods.txt |
|
0
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
44 -tda $tda |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
45 -t $t$precursor_ion_tol_units |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
46 -ti $advanced.isotope_low,$advanced.isotope_high |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
47 -m $advanced.m |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
48 -inst $inst |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
49 -e $e |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
50 -protocol $advanced.protocol |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
51 -ntt $ntt |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
52 -minLength $advanced.minLength |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
53 -maxLength $advanced.maxLength |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
54 -minCharge $advanced.minCharge |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
55 -maxCharge $advanced.maxCharge |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
56 -n $advanced.n |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
57 -addFeatures $advanced.addFeatures |
|
6
0a376f581288
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit 498437250b9fa438abd6865b7e9ba71298599ee7
galaxyp
parents:
5
diff
changeset
|
58 #if $tsvcheck |
|
0a376f581288
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit 498437250b9fa438abd6865b7e9ba71298599ee7
galaxyp
parents:
5
diff
changeset
|
59 && |
|
0a376f581288
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit 498437250b9fa438abd6865b7e9ba71298599ee7
galaxyp
parents:
5
diff
changeset
|
60 msgf_plus |
|
0a376f581288
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit 498437250b9fa438abd6865b7e9ba71298599ee7
galaxyp
parents:
5
diff
changeset
|
61 edu.ucsd.msjava.ui.MzIDToTsv |
|
0a376f581288
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit 498437250b9fa438abd6865b7e9ba71298599ee7
galaxyp
parents:
5
diff
changeset
|
62 -i '$output_name' |
|
0a376f581288
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit 498437250b9fa438abd6865b7e9ba71298599ee7
galaxyp
parents:
5
diff
changeset
|
63 -o output.tsv |
|
0a376f581288
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit 498437250b9fa438abd6865b7e9ba71298599ee7
galaxyp
parents:
5
diff
changeset
|
64 #end if |
|
0
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
65 && |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
66 mv '$output_name' output |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
67 ]]> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
68 </command> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
69 <inputs> |
|
5
468e8d70a073
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
4
diff
changeset
|
70 <conditional name="msgf_input"> |
|
468e8d70a073
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
4
diff
changeset
|
71 <param name="intype_selector" type="select" label="Type of MSGF+ analysis"> |
|
468e8d70a073
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
4
diff
changeset
|
72 <option value="single">Single database</option> |
|
468e8d70a073
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
4
diff
changeset
|
73 <option value="fractions">Prefractionated database</option> |
|
468e8d70a073
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
4
diff
changeset
|
74 </param> |
|
468e8d70a073
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
4
diff
changeset
|
75 <when value="single"> |
|
468e8d70a073
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
4
diff
changeset
|
76 <param argument="-s" type="data" format="mzml" label="Input Raw MS File(s)"/> |
|
468e8d70a073
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
4
diff
changeset
|
77 <param argument="-d" type="data" format="fasta" label="Protein Database" help="Select FASTA database from history"/> |
|
468e8d70a073
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
4
diff
changeset
|
78 </when> |
|
468e8d70a073
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
4
diff
changeset
|
79 <when value="fractions"> |
|
468e8d70a073
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
4
diff
changeset
|
80 <param name="db_spectra" type="data_collection" collection_type="paired" |
|
7
51fd56b09e64
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit b2712071afd2d74261bc3e3fc555355f5675a0d6
galaxyp
parents:
6
diff
changeset
|
81 label="Collection: Pairs of spectra (forward) and FASTA database (reverse)"/> |
|
5
468e8d70a073
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
4
diff
changeset
|
82 </when> |
|
468e8d70a073
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
4
diff
changeset
|
83 </conditional> |
|
6
0a376f581288
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit 498437250b9fa438abd6865b7e9ba71298599ee7
galaxyp
parents:
5
diff
changeset
|
84 <param name="tsvcheck" type="boolean" label="Output TSV as well?" /> |
|
0
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
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" /> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
86 <param argument="-t" type="float" value="10" label="Precursor mass tolerance" help="Error tolerance for matching peptide mass to precursor ion mass"/> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
87 <param name="precursor_ion_tol_units" type="select" label="Precursor mass tolerance units" help="Daltons are common for low-res instruments, ppm for high-res instruments"> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
88 <option value="ppm" selected="true">Parts per million (ppm)</option> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
89 <option value="Da">Daltons</option> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
90 </param> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
91 <param argument="-inst" label="Instrument type" type="select" help="The instrument type that generated the MS/MS spectra is used to determine the scoring model"> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
92 <option value="0" selected="true">Low-res (LCQ/LTQ)</option> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
93 <option value="1" >High-res (LTQ-Orbitrap)</option> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
94 <option value="2" >Q-TOF</option> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
95 <option value="3" >Q-Exactive</option> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
96 </param> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
97 <param argument="-e" type="select" label="Enzyme" help="Enzyme used to digest proteins in sample preparation; trypsin is the most commonly used enzyme"> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
98 <option value="0">Unspecific cleavage</option> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
99 <option value="1" selected="true">Trypsin, no P rule</option> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
100 <option value="2">Chymotrypsin, no P rule (FYWL)</option> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
101 <option value="3">Lys-C, no P rule</option> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
102 <option value="4">Lys-N</option> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
103 <option value="5">Glu-C (glutamyl endopeptidase)</option> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
104 <option value="6">Arg-C</option> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
105 <option value="7">Asp-N</option> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
106 <option value="8">Alpha-lytic protease</option> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
107 <option value="9">No enzyme</option> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
108 </param> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
109 <param argument="-ntt" type="select" format="text" label="Number of tolerable termini" help="Semi-specific requires more time than fully specific; non-specific requires much more."> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
110 <option value="2" selected="true">Fully specific (both termini match cleavage rules)</option> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
111 <option value="1">Semi-specific (at least one terminus must match cleavage rules)</option> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
112 <option value="0">Non-specific (neither terminus is required to match cleavage rules)</option> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
113 </param> |
|
1
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
114 |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
115 <param name="common_fixed_modifications" type="select" label="Common Fixed Modifications" multiple="true" help="Occurs in known places on peptide sequence. Hold the appropriate key while clicking to select multiple items"> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
116 <option value="C2H3N1O1_C_fix_any_Carbamidomethyl" selected="true">Carbamidomethyl C</option> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
117 <option value="144.102063_*_fix_N-term_iTRAQ4plex">iTRAQ 4-plex N-term</option> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
118 <option value="144.102063_K_fix_any_iTRAQ4plex">iTRAQ 4-plex K</option> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
119 <option value="225.155833_*_fix_N-term_TMT6plex">TMT 2-plex N-term</option> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
120 <option value="225.155833_K_fix_any_TMT6plex">TMT 2-plex K</option> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
121 <option value="229.162932_*_fix_N-term_TMT6plex">TMT 6-or-10-plex N-term</option> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
122 <option value="229.162932_K_fix_any_TMT6plex">TMT 6-or-10-plex K</option> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
123 <sanitizer invalid_char=""><valid initial="string.printable"><add value="["/><add value="]"/><add value=","/><add value="-"/></valid><mapping initial="none"></mapping></sanitizer> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
124 </param> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
125 <param name="common_variable_modifications" type="select" label="Common Variable Modifications" multiple="true" help="Can occur anywhere on the peptide sequence; adds additional error to search score. Hold the appropriate key while clicking to select multiple items"> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
126 <option value="C2H2O1_K_opt_any_Acetyl">Acetylation K</option> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
127 <option value="C2H2O_*_opt_Prot-N-term_Acetyl">Acetylation Protein N-term</option> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
128 <option value="C2H3NO_C_opt_any_Carbamidomethyl">Carbamidomethyl C</option> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
129 <option value="C2H3NO_*_opt_N-term_Carbamidomethyl">Carbamidomethyl N-term</option> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
130 <option value="H-1N-1O1_N_opt_any_Deamidated">Deamidation N</option> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
131 <option value="H-1N-1O1_Q_opt_any_Deamidated">Deamidation Q</option> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
132 <option value="CH2_K_opt_any_Methyl">Methylation K</option> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
133 <option value="O1_M_opt_any_Oxidation" selected="true">Oxidation M</option> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
134 <option value="HO3P_S_opt_any_Phospho">Phosphorylation S</option> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
135 <option value="HO3P_T_opt_any_Phospho">Phosphorylation T</option> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
136 <option value="HO3P_Y_opt_any_Phospho">Phosphorylation Y</option> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
137 <option value="H-2O-1_E_opt_N-term_Glu->pyro-Glu">Pyro-glu from E</option> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
138 <option value="H-3N-1_Q_opt_N-term_Gln->pyro-Glu">Pyro-glu from Q</option> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
139 <sanitizer invalid_char=""><valid initial="string.printable"><add value="["/><add value="]"/><add value=","/><add value="-"/></valid><mapping initial="none"></mapping></sanitizer> |
|
0
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
140 </param> |
|
1
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
141 |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
142 <repeat name="custom_mods" title="Custom Modifications" help="Specify modifications with custom parameters"> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
143 <param name="formula_or_mass" type="text" label="Formula or Mass"> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
144 <sanitizer> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
145 <valid initial="string.digits"> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
146 <add value="C"/> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
147 <add value="H"/> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
148 <add value="O"/> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
149 <add value="N"/> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
150 <add value="S"/> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
151 <add value="P"/> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
152 <add value="B"/><add value="r"/> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
153 <add value="C"/><add value="l"/> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
154 <add value="F"/><add value="e"/> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
155 <add value="S"/> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
156 <add value="."/> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
157 <add value="-"/> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
158 </valid> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
159 </sanitizer> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
160 </param> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
161 <param name="aa_specificity" type="select" multiple="true" label="Amino Acid Specificity"> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
162 <option value="*" selected="true">Any</option> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
163 <option value="A">A</option> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
164 <option value="C">C</option> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
165 <option value="D">D</option> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
166 <option value="E">E</option> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
167 <option value="F">F</option> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
168 <option value="G">G</option> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
169 <option value="H">H</option> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
170 <option value="I">I</option> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
171 <option value="K">K</option> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
172 <option value="L">L</option> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
173 <option value="M">M</option> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
174 <option value="N">N</option> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
175 <option value="P">P</option> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
176 <option value="Q">Q</option> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
177 <option value="R">R</option> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
178 <option value="S">S</option> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
179 <option value="T">T</option> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
180 <option value="V">V</option> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
181 <option value="W">W</option> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
182 <option value="Y">Y</option> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
183 </param> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
184 <param name="fix_or_opt" type="select" label="Variable or Fixed?"> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
185 <option value="opt" selected="true">Variable</option> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
186 <option value="fix">Fixed</option> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
187 </param> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
188 <param name="position_specificity" type="select" label="Positional Specificity"> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
189 <option value="any" selected="true">Any</option> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
190 <option value="n-term">Peptide N-terminal</option> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
191 <option value="c-term">Peptide C-terminal</option> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
192 <option value="prot-n-term">Protein N-terminal</option> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
193 <option value="prot-c-term">Protein C-terminal</option> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
194 </param> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
195 <param name="mod_name" type="text" label="Name" help="If this mod has an entry there in Unimod, this name should match its name there" /> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
196 </repeat> |
|
0
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
197 |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
198 <!-- MS-GF+ ADVANCED PARAMETERS --> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
199 <section name="advanced" title="Advanced Options"> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
200 <param argument="-minCharge" label="Minimum precursor charge" value="2" type="integer" help="Minimum precursor charge to consider if charges are not specified in the spectrum file"/> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
201 <param argument="-maxCharge" label="Maximum precursor charge" value="3" type="integer" help="Maximum precursor charge to consider if charges are not specified in the spectrum file"/> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
202 <param argument="-minLength" label="Minimum peptide length" value="6" type="integer" help="Minimum peptide length to consider"/> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
203 <param argument="-maxLength" label="Maximum peptide length" value="40" type="integer" help="Maximum peptide length to consider"/> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
204 <param name="num_ptms" label="Maximum modifications allowed per peptide" type="integer" value="2" /> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
205 <param argument="-m" label="Fragmentation type" type="select" help="Fragmentation method identifier (used to determine the scoring model)"> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
206 <option value="0" selected="True">As written in the spectrum or CID if no info</option> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
207 <option value="1" >CID</option> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
208 <option value="2" >ETD</option> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
209 <option value="3" >HCD</option> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
210 </param> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
211 <param argument="-protocol" label="Protocol type" type="select" help="Protocols are used to enable scoring parameters for enriched and/or labeled samples"> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
212 <option value="0" selected="True">Automatic</option> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
213 <option value="1" >Phosphorylation</option> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
214 <option value="2" >iTRAQ</option> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
215 <option value="3" >iTRAQPhospho</option> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
216 <option value="4" >TMT</option> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
217 <option value="5" >Standard</option> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
218 </param> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
219 <param argument="-n" label="Maximum matches per spectrum" type="integer" value="1" help="Number of peptide matches per spectrum to report" /> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
220 <param argument="-addFeatures" label="Calculate additional scoring features?" type="boolean" truevalue="1" falsevalue="0" help="If true, several extra derivative scores are calculated for each match" /> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
221 <param name="isotope_low" label="Lower isotope error range" type="integer" value="0" help="Takes into account of the error introduced by chooosing a non-monoisotopic peak for fragmentation (-ti)" /> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
222 <param name="isotope_high" label="Upper isotope error range" type="integer" value="1" /> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
223 </section> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
224 </inputs> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
225 <outputs> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
226 <data name="output" format="mzid" from_work_dir="output" /> |
|
6
0a376f581288
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit 498437250b9fa438abd6865b7e9ba71298599ee7
galaxyp
parents:
5
diff
changeset
|
227 <data name="tsvoutput" format="tabular" from_work_dir="output.tsv" > |
|
0a376f581288
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit 498437250b9fa438abd6865b7e9ba71298599ee7
galaxyp
parents:
5
diff
changeset
|
228 <filter>tsvcheck</filter> |
|
0a376f581288
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit 498437250b9fa438abd6865b7e9ba71298599ee7
galaxyp
parents:
5
diff
changeset
|
229 </data> |
|
0
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
230 </outputs> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
231 <tests> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
232 <test> |
|
6
0a376f581288
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit 498437250b9fa438abd6865b7e9ba71298599ee7
galaxyp
parents:
5
diff
changeset
|
233 <param name="msgf_input|intype_selector" value="single" /> |
|
0a376f581288
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit 498437250b9fa438abd6865b7e9ba71298599ee7
galaxyp
parents:
5
diff
changeset
|
234 <param name="msgf_input|s" value="input/201208-378803.mzML" ftype="mzml" /> |
|
0a376f581288
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit 498437250b9fa438abd6865b7e9ba71298599ee7
galaxyp
parents:
5
diff
changeset
|
235 <param name="msgf_input|d" value="input/cow.protein.PRG2012-subset.fasta" ftype="fasta" /> |
|
5
468e8d70a073
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
4
diff
changeset
|
236 <param name="tda" value="1" /> |
|
468e8d70a073
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
4
diff
changeset
|
237 <param name="ntt" value="1" /> |
|
468e8d70a073
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
4
diff
changeset
|
238 <param name="t" value="50" /> |
|
468e8d70a073
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
4
diff
changeset
|
239 <param name="precursor_ion_tol_units" value="ppm" /> |
|
468e8d70a073
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
4
diff
changeset
|
240 <param name="common_fixed_modifications" value="" /> |
|
468e8d70a073
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
4
diff
changeset
|
241 <param name="common_variable_modifications" value="" /> |
|
468e8d70a073
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
4
diff
changeset
|
242 <output name="output" file="201208-378803-msgf_20161026-50ppm-semitryptic-no_mods.mzid" compare="sim_size" delta="20" /> |
|
468e8d70a073
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
4
diff
changeset
|
243 </test> |
|
468e8d70a073
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
4
diff
changeset
|
244 <test> |
|
6
0a376f581288
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit 498437250b9fa438abd6865b7e9ba71298599ee7
galaxyp
parents:
5
diff
changeset
|
245 <param name="msgf_input|intype_selector" value="single" /> |
|
0a376f581288
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit 498437250b9fa438abd6865b7e9ba71298599ee7
galaxyp
parents:
5
diff
changeset
|
246 <param name="msgf_input|s" value="input/201208-378803.mzML" /> |
|
0a376f581288
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit 498437250b9fa438abd6865b7e9ba71298599ee7
galaxyp
parents:
5
diff
changeset
|
247 <param name="msgf_input|d" value="input/cow.protein.PRG2012-subset.fasta" /> |
|
0a376f581288
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit 498437250b9fa438abd6865b7e9ba71298599ee7
galaxyp
parents:
5
diff
changeset
|
248 <param name="tsvcheck" value="true" /> |
|
0a376f581288
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit 498437250b9fa438abd6865b7e9ba71298599ee7
galaxyp
parents:
5
diff
changeset
|
249 <param name="tda" value="1" /> |
|
0a376f581288
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit 498437250b9fa438abd6865b7e9ba71298599ee7
galaxyp
parents:
5
diff
changeset
|
250 <param name="ntt" value="1" /> |
|
0a376f581288
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit 498437250b9fa438abd6865b7e9ba71298599ee7
galaxyp
parents:
5
diff
changeset
|
251 <param name="t" value="50" /> |
|
0a376f581288
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit 498437250b9fa438abd6865b7e9ba71298599ee7
galaxyp
parents:
5
diff
changeset
|
252 <param name="precursor_ion_tol_units" value="ppm" /> |
|
0a376f581288
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit 498437250b9fa438abd6865b7e9ba71298599ee7
galaxyp
parents:
5
diff
changeset
|
253 <param name="common_fixed_modifications" value="" /> |
|
0a376f581288
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit 498437250b9fa438abd6865b7e9ba71298599ee7
galaxyp
parents:
5
diff
changeset
|
254 <param name="common_variable_modifications" value="" /> |
|
0a376f581288
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit 498437250b9fa438abd6865b7e9ba71298599ee7
galaxyp
parents:
5
diff
changeset
|
255 <output name="output" file="201208-378803-msgf_20161026-50ppm-semitryptic-no_mods.mzid" compare="sim_size" delta="20" /> |
|
0a376f581288
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit 498437250b9fa438abd6865b7e9ba71298599ee7
galaxyp
parents:
5
diff
changeset
|
256 <output name="tsvoutput" file="201208-378803-msgf_20161026-50ppm-semitryptic-no_mods.tsv" compare="sim_size" delta="20" /> |
|
0a376f581288
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit 498437250b9fa438abd6865b7e9ba71298599ee7
galaxyp
parents:
5
diff
changeset
|
257 </test> |
|
0a376f581288
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit 498437250b9fa438abd6865b7e9ba71298599ee7
galaxyp
parents:
5
diff
changeset
|
258 <test> |
|
0a376f581288
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit 498437250b9fa438abd6865b7e9ba71298599ee7
galaxyp
parents:
5
diff
changeset
|
259 <param name="msgf_input|intype_selector" value="fractions" /> |
|
0a376f581288
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit 498437250b9fa438abd6865b7e9ba71298599ee7
galaxyp
parents:
5
diff
changeset
|
260 <param name="msgf_input|db_spectra"> |
|
0a376f581288
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit 498437250b9fa438abd6865b7e9ba71298599ee7
galaxyp
parents:
5
diff
changeset
|
261 <collection type="paired"> |
|
0a376f581288
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit 498437250b9fa438abd6865b7e9ba71298599ee7
galaxyp
parents:
5
diff
changeset
|
262 <element name="forward" value="input/201208-378803.mzML" /> |
|
0a376f581288
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit 498437250b9fa438abd6865b7e9ba71298599ee7
galaxyp
parents:
5
diff
changeset
|
263 <element name="reverse" value="input/cow.protein.PRG2012-subset.fasta" /> |
|
0a376f581288
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit 498437250b9fa438abd6865b7e9ba71298599ee7
galaxyp
parents:
5
diff
changeset
|
264 </collection> |
|
0a376f581288
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit 498437250b9fa438abd6865b7e9ba71298599ee7
galaxyp
parents:
5
diff
changeset
|
265 </param> |
|
1
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
266 <param name="tda" value="1" /> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
267 <param name="ntt" value="1" /> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
268 <param name="t" value="50" /> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
269 <param name="precursor_ion_tol_units" value="ppm" /> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
270 <param name="common_fixed_modifications" value="" /> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
271 <param name="common_variable_modifications" value="" /> |
|
7
51fd56b09e64
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit b2712071afd2d74261bc3e3fc555355f5675a0d6
galaxyp
parents:
6
diff
changeset
|
272 <output name="output" file="201208-378803-msgf_20161026-50ppm-semitryptic-no_mods.mzid" compare="sim_size" delta="100" /> |
|
0
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
273 </test> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
274 <test> |
|
6
0a376f581288
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit 498437250b9fa438abd6865b7e9ba71298599ee7
galaxyp
parents:
5
diff
changeset
|
275 <param name="msgf_input|intype_selector" value="single" /> |
|
0a376f581288
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit 498437250b9fa438abd6865b7e9ba71298599ee7
galaxyp
parents:
5
diff
changeset
|
276 <param name="msgf_input|s" value="input/201208-378803.mzML" /> |
|
0a376f581288
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit 498437250b9fa438abd6865b7e9ba71298599ee7
galaxyp
parents:
5
diff
changeset
|
277 <param name="msgf_input|d" value="input/cow.protein.PRG2012-subset.fasta" /> |
|
0
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
278 <param name="tda" value="1" /> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
279 <param name="t" value="0.02" /> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
280 <param name="precursor_ion_tol_units" value="Da" /> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
281 <param name="isotope_low" value="-1" /> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
282 <param name="isotope_high" value="0" /> |
|
1
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
283 <param name="m" value="3" /> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
284 <param name="inst" value="2" /> |
|
0
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
285 <param name="e" value="3" /> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
286 <param name="protocol" value="2" /> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
287 <param name="minLength" value="10" /> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
288 <param name="maxLength" value="20" /> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
289 <param name="minCharge" value="2" /> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
290 <param name="maxCharge" value="6" /> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
291 <param name="n" value="2" /> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
292 <param name="addFeatures" value="1" /> |
|
1
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
293 |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
294 <param name="common_fixed_modifications" value="C2H3N1O1_C_fix_any_Carbamidomethyl,144.102063_*_fix_N-term_iTRAQ4plex,144.102063_K_fix_any_iTRAQ4plex" /> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
295 <param name="common_variable_modifications" value="O1_M_opt_any_Oxidation,H-3N-1_Q_opt_N-term_Gln->pyro-Glu" /> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
296 |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
297 <param name="custom_mods_0|formula_or_mass" value="C-2H-2O-2" /> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
298 <param name="custom_mods_0|aa_specificity" value="G" /> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
299 <param name="custom_mods_0|fix_or_opt" value="opt" /> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
300 <param name="custom_mods_0|position_specificity" value="c-term" /> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
301 <param name="custom_mods_0|mod_name" value="Gly-loss+Amide" /> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
302 |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
303 <param name="custom_mods_1|formula_or_mass" value="C10H10N5O7P" /> |
|
5
468e8d70a073
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
4
diff
changeset
|
304 <param name="custom_mods_1|aa_specificity" value="C,S" /> |
|
1
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
305 <param name="custom_mods_1|fix_or_opt" value="opt" /> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
306 <param name="custom_mods_1|position_specificity" value="any" /> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
307 <param name="custom_mods_1|mod_name" value="cGMP" /> |
|
08b316ae9ec4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents:
0
diff
changeset
|
308 |
|
5
468e8d70a073
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
4
diff
changeset
|
309 <output name="output" file="201208-378803-msgf_20161026-2mmu-tryptic-many_mods.mzid" lines_diff="6" /> |
|
0
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
310 </test> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
311 </tests> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
312 <help> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
313 **What it does** |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
314 |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
315 Performs protein identification via database search using MS-GF+. |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
316 |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
317 </help> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
318 <citations> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
319 <citation type="doi">10.1038/ncomms6277</citation> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
320 <citation type="doi">10.1021/pr8001244</citation> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
321 <citation type="bibtex">@misc{toolsGalaxyP, author = {Chilton, J, Gruening, B, Chambers, MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub repository}, |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
322 year = {2015}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}</citation> <!-- TODO: fix substitution of commit ", commit = {$sha1$}" --> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
323 </citations> |
|
dbc77b37e20f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
galaxyp
parents:
diff
changeset
|
324 </tool> |