Mercurial > repos > iracooke > mascot
diff mascot.xml @ 8:f567d1818b84 draft
Docker support and update for protk 1.4
| author | iracooke |
|---|---|
| date | Thu, 26 Mar 2015 20:04:50 -0400 |
| parents | 75184e45bf84 |
| children | 54c7e3593aac |
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--- a/mascot.xml Fri Jun 13 18:26:31 2014 -0400 +++ b/mascot.xml Thu Mar 26 20:04:50 2015 -0400 @@ -1,7 +1,8 @@ -<tool id="proteomics_search_mascot_1" name="Mascot MSMS Search" version="1.0.2"> +<tool id="proteomics_search_mascot_1" name="Mascot MSMS Search" version="1.1.0"> <requirements> - <requirement type="package" version="1.3">protk</requirement> + <container type="docker">iracooke/protk-1.4.1</container> + <requirement type="package" version="1.4">protk</requirement> </requirements> <description>Mascot MS/MS Search</description> @@ -31,19 +32,26 @@ --fix-mods=' $fixed_mods - ' - --allowed-charges=$allowed_charges + ' + + --allowed-charges='$allowed_charges' --enzyme=$enzyme - --instrument=$instrument + --instrument='$instrument' + -p $precursor_ion_tol + --precursor-ion-tol-units=$precursor_tolu + #if $email --email=$email + #end if -v $missed_cleavages + --quantitation='$quant_method' + #if $security.security_use --use-security --username $security.username @@ -54,6 +62,8 @@ --proxy $proxy #end if + --timeout=600 + </command> <inputs> @@ -63,7 +73,7 @@ <conditional name="database"> <param name="source_select" type="select" label="Database Type"> <option value="built_in">Built-In</option> - <option value="custom_defined">Custom</option> + <option selected="true" value="custom_defined">Custom</option> </param> <when value="built_in"> <param name="dbkey" type="select" format="text" > @@ -97,7 +107,7 @@ <label>Missed Cleavages Allowed</label> <option value="0">0</option> <option value="1">1</option> - <option value="2">2</option> + <option selected="true" value="2">2</option> </param> <param name="enzyme" type="select" format="text"> @@ -143,7 +153,7 @@ <option value="1+, 2+ and 3+">1+,2+ and 3+</option> <option value="2+">2+</option> <option value="2+ and 3+">2+ and 3+</option> - <option value="2+,3+ and 4+">2+,3+ and 4+</option> + <option selected="true" value="2+,3+ and 4+">2+,3+ and 4+</option> <option value="3+">3+</option> <option value="4+">4+</option> <option value="5+">5+</option> @@ -156,7 +166,7 @@ <label>Instrument</label> <option value="ESI-QUAD-TOF">ESI-QUAD-TOF</option> <option value="MALDI-TOF-PSD">MALDI-TOF-PSD</option> - <option value="ESI-TRAP">ESI-TRAP</option> + <option selected="true" value="ESI-TRAP">ESI-TRAP</option> <option value="ESI-QUAD">ESI-QUAD</option> <option value="ESI-FTICR">ESI-FTICR</option> <option value="MALDI-TOF-TOF">MALDI-TOF-TOF</option> @@ -168,10 +178,44 @@ <option value="MALDI-ISD">MALDI-ISD</option> <option value="CID+ETD">CID+ETD</option> </param> + + + <param name="quant_method" type="select" format="text"> + <label>Quantitation</label> + <option selected="true" value="None">None</option> + <option value="iTRAQ 4plex">iTRAQ 4plex</option> + <option value="iTRAQ 4plex (protein)">iTRAQ 4plex (protein)</option> + <option value="iTRAQ 8plex">iTRAQ 8plex</option> + <option value="TMT 6plex">TMT 6plex</option> + <option value="TMT 2plex">TMT 2plex</option> + <option value="DiLeu 4plex">DiLeu 4plex</option> + <option value="18O multiplex">18O multiplex</option> + <option value="SILAC K+6 R+6 multiplex">SILAC K+6 R+6 multiplex</option> + <option value="IPTL (Succinyl and IMID) multiplex">IPTL (Succinyl and IMID) multiplex</option> + <option value="ICPL duplex pre-digest [MD]">ICPL duplex pre-digest [MD]</option> + <option value="ICPL duplex post-digest [MD]">ICPL duplex post-digest [MD]</option> + <option value="ICPL triplex pre-digest [MD]">ICPL triplex pre-digest [MD]</option> + <option value="ICPL quadruplex pre-digest [MD]">ICPL quadruplex pre-digest [MD]</option> + <option value="18O corrected [MD]">18O corrected [MD]</option> + <option value="15N Metabolic [MD]">15N Metabolic [MD]</option> + <option value="15N + 13C Metabolic [MD]">15N + 13C Metabolic [MD]</option> + <option value="SILAC K+6 R+10 [MD]">SILAC K+6 R+10 [MD]</option> + <option value="SILAC K+6 R+10 Arg-Pro [MD]">SILAC K+6 R+10 Arg-Pro [MD]</option> + <option value="SILAC K+6 R+6 [MD]">SILAC K+6 R+6 [MD]</option> + <option value="SILAC R+6 R+10 [MD]">SILAC R+6 R+10 [MD]</option> + <option value="SILAC K+8 R+10 [MD]">SILAC K+8 R+10 [MD]</option> + <option value="SILAC K+4 K+8 R+6 R+10 [MD]">SILAC K+4 K+8 R+6 R+10 [MD]</option> + <option value="ICAT ABI Cleavable [MD]">ICAT ABI Cleavable [MD]</option> + <option value="ICAT D8 [MD]">ICAT D8 [MD]</option> + <option value="Dimethylation [MD]">Dimethylation [MD]</option> + <option value="NBS Shimadzu [MD]">NBS Shimadzu [MD]</option> + <option value="Acetylation [MD]">Acetylation [MD]</option> + <option value="Label-free [MD]">Label-free [MD]</option> + </param> - <param name="fragment_ion_tol" label="Fragment Ion Tolerance" type="float" value="0.65" min="0" max="10000" help="Fragment ion tolerance in Daltons"/> + <param name="fragment_ion_tol" label="Fragment Ion Tolerance" type="float" value="0.5" min="0" max="10000" help="Fragment ion tolerance in Daltons"/> - <param name="precursor_ion_tol" label="Precursor Ion Tolerance (Da or ppm)" type="float" value="100" min="0" max="10000" help="Enter a value in Daltons or ppm depending on the units chosen below"/> + <param name="precursor_ion_tol" label="Precursor Ion Tolerance (Da or ppm)" type="float" value="10" min="0" max="10000" help="Enter a value in Daltons or ppm depending on the units chosen below"/> <param name="precursor_tolu" type="select" format="text"> <label>Precursor Ion Tolerance Units</label> <option value="ppm">ppm</option>