Mercurial > repos > galaxyp > idpqonvert
annotate idpQonvertEmbedder.xml @ 5:feebe32c3a52 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0a0c1b53f934a0edfc7f18e9c401ad353a44092a
| author | galaxyp |
|---|---|
| date | Fri, 22 Sep 2017 10:46:42 -0400 |
| parents | d1f7b2395bc2 |
| children | aec819a9068b |
| rev | line source |
|---|---|
|
3
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
1 <?xml version="1.0"?> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
2 <tool id="idpqonvertEmbedder" name="idpEmbedder" version="@VERSION@.0"> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
3 <description>Embed human/mouse gene metadata into IDPicker files</description> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
4 <macros> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
5 <import>macros.xml</import> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
6 </macros> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
7 <expand macro="requirements" /> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
8 <stdio> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
9 <exit_code range="1:" level="fatal" description="Job Failed" /> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
10 <regex match="\nError:.*\n" source="both" level="fatal" /> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
11 </stdio> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
12 <command> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
13 <![CDATA[ |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
14 #set $input_name = $input.display_name |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
15 cp '$input' output && |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
16 ln -s output output.idpDB && |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
17 ln -s \$(dirname \$(which idpQonvert))/gene2protein.db3 gene2protein.db3 && |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
18 |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
19 #if $use_raw_data_condition.use_raw_data |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
20 #for $i in $use_raw_data_condition.input_raw |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
21 ln -s '${i.file_name}' '${i.display_name}' && |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
22 #end for |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
23 #end if |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
24 |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
25 idpQonvert |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
26 -EmbedOnly true |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
27 -EmbedGeneMetadata $EmbedGeneMetadata |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
28 #if $use_raw_data_condition.use_raw_data |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
29 -EmbedSpectrumScanTimes $use_raw_data_condition.EmbedSpectrumScanTimes |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
30 -EmbedSpectrumSources $use_raw_data_condition.EmbedSpectrumSources |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
31 -QuantitationMethod $use_raw_data_condition.QuantitationMethod |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
32 #end if |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
33 output.idpDB |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
34 ]]> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
35 </command> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
36 <inputs> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
37 <param name="input" type="data" format="idpdb" label="Input idpDB file" /> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
38 <param argument="-EmbedGeneMetadata" type="boolean" value="true" label="Embed Gene Metadata?" help="Allows gene-centric analysis in IDPicker. The gene metadata embedding only works for human/mouse proteins from a RefSeq database. For best results, run idpQonvert with RefSeq no matter what database was used for the search: idpQonvert always remap the peptides anyway. Non-human/mouse proteins and any unmappable human/mouse proteins will get gene ids like "Unmapped_<protein accession>". This option, run by itself, is very fast." /> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
39 <conditional name="use_raw_data_condition"> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
40 <param name="use_raw_data" type="boolean" label="Do you have the raw data (spectra)?" help="More embed options are available if the raw spectra are available." /> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
41 <when value="false"></when> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
42 <when value="true"> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
43 <param name="input_raw" type="data" format="mzml,mzxml,mgf,ms2,mz5" label="Input raw MS files" multiple="true" /> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
44 <param argument="-EmbedSpectrumSources" type="boolean" value="false" label="Embed Spectrum Sources?" help="Allows visualizing peptide-spectrum-matches without downloading the raw data. Embedding spectra will greatly increase the size of the database, even though only spectra that passed the import FDR filter will be included. This option can take a LONG time to run." /> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
45 <param argument="-EmbedSpectrumScanTimes" type="boolean" value="false" label="Embed Spectrum Scan Times?" help="If the pepXML/mzIdentML file did not contain scan time (retention time) information, this will look up that information in the raw data. This option, run by itself, will take some time (it has to open every raw file)." /> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
46 <param argument="-QuantitationMethod" type="select" label="Quantitation Method" help="Enables quantitation methods other than spectral counting. For isobaric isotope labelling quantitation (iTRAQ/TMT) or intensity-based label-free quantitation (XIC), select the appropriate QuantitationMethod here. You have to keep iTRAQ/TMT and label-free data separate since you can only specify a single QuantitationMethod for the entire assembly. Like embedding spectrum sources, this option can take a LONG time to run, although not quite as long."> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
47 <option value="None" selected="true">None</option> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
48 <option value="LabelFree">Label-free (XIC)</option> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
49 <option value="ITRAQ4plex">iTRAQ 4-plex</option> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
50 <option value="ITRAQ8plex">iTRAQ 8-plex</option> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
51 <option value="TMT2plex">TMT 2-plex</option> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
52 <option value="TMT6plex">TMT 6-plex</option> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
53 <option value="TMT10plex">TMT 10-plex</option> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
54 </param> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
55 </when> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
56 </conditional> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
57 </inputs> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
58 <outputs> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
59 <data format="idpdb" name="output" from_work_dir="output" /> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
60 </outputs> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
61 <tests> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
62 <test> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
63 <param name="input" value="input/201208-378803.idpDB" /> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
64 <param name="EmbedGeneMetadata" value="false" /> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
65 <output name="output" file="input/201208-378803.idpDB" compare="sim_size" delta="500000" /> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
66 </test> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
67 <test> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
68 <param name="input" value="input/201208-378803.idpDB" /> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
69 <param name="EmbedGeneMetadata" value="true" /> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
70 <output name="output" file="201208-378803-embeddedGenes.idpDB" compare="sim_size" delta="500000" /> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
71 </test> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
72 <test> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
73 <param name="input" value="input/201208-378803.idpDB" /> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
74 <param name="EmbedGeneMetadata" value="true" /> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
75 <param name="use_raw_data" value="true" /> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
76 <param name="input_raw" value="input/201208-378803.mzML" /> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
77 <param name="EmbedSpectrumSources" value="false" /> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
78 <param name="EmbedSpectrumScanTimes" value="true" /> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
79 <param name="QuantitationMethod" value="None" /> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
80 <output name="output" file="201208-378803-embeddedGenesAndScanTimes.idpDB" compare="sim_size" delta="500000" /> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
81 </test> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
82 <test> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
83 <param name="input" value="input/201208-378803.idpDB" /> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
84 <param name="EmbedGeneMetadata" value="true" /> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
85 <param name="use_raw_data" value="true" /> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
86 <param name="input_raw" value="input/201208-378803.mzML" /> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
87 <param name="EmbedSpectrumSources" value="true" /> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
88 <param name="EmbedSpectrumScanTimes" value="false" /> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
89 <param name="QuantitationMethod" value="None" /> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
90 <output name="output" file="201208-378803-embeddedGenesAndSpectra.idpDB" compare="sim_size" delta="500000" /> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
91 </test> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
92 <test> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
93 <param name="input" value="input/201208-378803.idpDB" /> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
94 <param name="EmbedGeneMetadata" value="true" /> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
95 <param name="use_raw_data" value="true" /> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
96 <param name="input_raw" value="input/201208-378803.mzML" /> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
97 <param name="EmbedSpectrumSources" value="false" /> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
98 <param name="EmbedSpectrumScanTimes" value="true" /> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
99 <param name="QuantitationMethod" value="ITRAQ4plex" /> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
100 <output name="output" file="201208-378803-embeddedGenesAndQuantitation.idpDB" compare="sim_size" delta="500000" /> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
101 </test> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
102 </tests> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
103 <help> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
104 <![CDATA[ |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
105 **What it does** |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
106 |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
107 Embeds optional data and metadata into the IDPicker 3 idpDB files. This should be run after all idpDB files have been merged together (e.g. after idpAssemble). |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
108 ]]> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
109 </help> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
110 <citations> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
111 <citation type="doi">10.1021/pr900360j</citation> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
112 <citation type="bibtex">@misc{toolsGalaxyP, author = {Chilton, J, Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub repository}, |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
113 year = {2015}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}</citation> <!-- TODO: fix substitution of commit ", commit = {$sha1$}" --> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
114 </citations> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
115 </tool> |