| Previous changeset 3:88495b2a6957 (2014-01-10) Next changeset 5:600b56d80ae3 (2014-01-10) |
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Commit message:
Putting back old fix |
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modified:
masscomb_dbsearch_xtandem.xml |
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| diff -r 88495b2a6957 -r b34fb7461546 masscomb_dbsearch_xtandem.xml --- a/masscomb_dbsearch_xtandem.xml Fri Jan 10 17:03:50 2014 +0100 +++ b/masscomb_dbsearch_xtandem.xml Fri Jan 10 17:35:38 2014 +0100 |
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| @@ -1,5 +1,9 @@ <tool name="X!Tandem" id="masscomb_xtandem200" version="2.0.0"> <description>MS/MS DB search</description> + <requirements> + <requirement type="set_environment">XTANDEM_12_10_01_PATH</requirement> + <requirement type="package" version="12.10011">xtandem</requirement> + </requirements> <!-- For remote debugging start you listener on port 8000 and use the following as command interpreter: java -jar -Xdebug -Xrunjdwp:transport=dt_socket,address=D0100564.wurnet.nl:8000 @@ -72,7 +76,7 @@ <option value="45.987721@C,224.152478@K,224.152478@[">Methylthio + TMT (C,K,nt)</option> <option value="45.987721@C,225.155833@K,225.155833@[">Methylthio + TMT2plex (C,K,nt)</option> <option value="45.987721@C,229.1629328@K,229.1629328@[">Methylthio + TMT6plex (C,K,nt)</option> - <option value="14.0156@],14.0156@D,14.0156@E">Methy +14Da (D,E,C-term)</option> + <option value="14.0156@],14.0156@D,14.0156@E">Methy +14Da (D,E,C-term)</option> </param> <param name="potential_modifications" type="select" display="checkboxes" multiple="true" label="Potential modifications" help=""> <option value="15.994915@M">Oxidation (M)</option> @@ -206,7 +210,7 @@ <tns:Program xmlns:tns="http://masscomb.pri.com/toolparameters/" name="XTandemWrapper" program="XTandemWrapper"> <Files/> <Parameters> - <Attribute attributeName="xtandemLocation" value="/home/lukas007/galaxy-dist/tool-data/prims/tandem-linux-12-10-01-1/bin/" type="Unknown" description=""/> + <Attribute attributeName="xtandemLocation" value="\${XTANDEM_12_10_01_PATH}/bin" type="Unknown" description=""/> <Attribute attributeName="database" value="${database}" type="Unknown" description=""/> <Attribute attributeName="precursor_mass_tolerance_lower" toolSpecificName="spectrum, parent monoisotopic mass error minus" value="${precursor_mass_tolerance_lower}" type="Unknown" description=""/> <Attribute attributeName="precursor_mass_tolerance_upper" toolSpecificName="spectrum, parent monoisotopic mass error plus" value="${precursor_mass_tolerance_upper}" type="Unknown" description=""/> |