Mercurial > repos > iracooke > xtandem
diff tandem.xml @ 14:9d6e0ad4d600 draft
Docker support and update for protk 1.4
| author | iracooke |
|---|---|
| date | Thu, 26 Mar 2015 19:53:53 -0400 |
| parents | c60d1f18fd85 |
| children | 0faaab4f192a |
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--- a/tandem.xml Tue Jul 01 11:06:33 2014 -0400 +++ b/tandem.xml Thu Mar 26 19:53:53 2015 -0400 @@ -1,7 +1,8 @@ -<tool id="proteomics_search_tandem_1" name="X!Tandem MSMS Search" version="1.0.2"> +<tool id="proteomics_search_tandem_1" name="X!Tandem MSMS Search" version="1.1.0"> <requirements> - <requirement type="package" version="1.3.0">protk</requirement> + <container type="docker">iracooke/protk-1.4.1</container> + <requirement type="package" version="1.4">protk</requirement> </requirements> <description>Run an X!Tandem Search</description> @@ -44,7 +45,7 @@ -f $fragment_ion_tol - -p $precursor_ion_tol + -p $precursor_ion_tol $allow_multi_isotope_search @@ -86,9 +87,9 @@ <when value="built_in"> <param name="paramskey" type="select" format="text" > <label>Paramset</label> - <option value="gpm">GPM</option> + <option value="isb_kscore">ISB K-Score (Recommended for TPP)</option> <option value="isb_native">ISB Native</option> - <option value="isb_kscore">ISB K-Score</option> + <option value="gpm">GPM</option> </param> </when> <when value="input_ref"> @@ -132,7 +133,7 @@ <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="cleavage_semi" type="boolean" label="Allow semi-cleaved peptides" help="This can increase search time dramatically" truevalue="--cleavage-semi" falsevalue=""/> @@ -143,42 +144,42 @@ <param name="enzyme" type="select" format="text"> <label>Enzyme</label> - <option value="[R]|{P}">argc - [R]|{P}</option> - <option value="[X]|[D]">aspn - [X]|[D]</option> - <option value="[FLMWY]|{P}">chymotrypsin - [FLMWY]|{P}</option> - <option value="[R]|[X]">clostripain - [R]|[X]</option> - <option value="[M]|{P}">cnbr - [M]|{P}</option> - <option value="[AGILV]|{P}">elastase - [AGILV]|{P}</option> - <option value="[D]|{P}">formicacid - [D]|{P}</option> - <option value="[DE]|{P}">gluc - [DE]|{P}</option> - <option value="[E]|{P}">gluc_bicarb - [E]|{P}</option> - <option value="[W]|[X]">iodosobenzoate - [W]|[X]</option> - <option value="[K]|{P}">lysc - [K]|{P}</option> - <option value="[K]|[X]">lysc-p - [K]|[X]</option> - <option value="[X]|[K]">lysn - [X]|[K]</option> - <option value="[X]|[AKRS]">lysn_promisc - [X]|[AKRS]</option> - <option value="[X]|[X]">nonspecific - [X]|[X]</option> - <option value="[FL]|[X]">pepsina - [FL]|[X]</option> - <option value="[P]|[X]">protein_endopeptidase - [P]|[X]</option> - <option value="[E]|[X]">staph_protease - [E]|[X]</option> - <option value="[FMWY]|{P},[KR]|{P},[X]|[D]">tca - [FMWY]|{P},[KR]|{P},[X]|[D]</option> - <option value="[KR]|{P}" selected="true">trypsin - [KR]|{P}</option> - <option value="[FKLMRWY]|{P}">trypsin/chymotrypsin - [FKLMRWY]|{P}</option> - <option value="[KR]|{P},[M]|{P}">trypsin/cnbr - [KR]|{P},[M]|{P}</option> - <option value="[DEKR]|{P}">trypsin_gluc - [DEKR]|{P}</option> + <option value="[R]__pc__{P}">argc - [R]|{P}</option> + <option value="[X]__pc__[D]">aspn - [X]|[D]</option> + <option value="[FLMWY]__pc__{P}">chymotrypsin - [FLMWY]|{P}</option> + <option value="[R]__pc__[X]">clostripain - [R]|[X]</option> + <option value="[M]__pc__{X}">cnbr - [M]|{X}</option> + <option value="[AGILV]__pc__{P}">elastase - [AGILV]|{P}</option> + <option value="[D]__pc__{P}">formicacid - [D]|{P}</option> + <option value="[DE]__pc__{P}">gluc - [DE]|{P}</option> + <option value="[E]__pc__{P}">gluc_bicarb - [E]|{P}</option> + <option value="[W]__pc__[X]">iodosobenzoate - [W]|[X]</option> + <option value="[K]__pc__{P}">lysc - [K]|{P}</option> + <option value="[K]__pc__[X]">lysc-p - [K]|[X]</option> + <option value="[X]__pc__[K]">lysn - [X]|[K]</option> + <option value="[X]__pc__[AKRS]">lysn_promisc - [X]|[AKRS]</option> + <option value="[X]__pc__[X]">nonspecific - [X]|[X]</option> + <option value="[FL]__pc__[X]">pepsina - [FL]|[X]</option> + <option value="[P]__pc__[X]">protein_endopeptidase - [P]|[X]</option> + <option value="[E]__pc__[X]">staph_protease - [E]|[X]</option> + <option value="[FMWY]__pc__{P},[KR]__pc__{P},[X]__pc__[D]">tca - [FMWY]|{P},[KR]|{P},[X]|[D]</option> + <option value="[KR]__pc__{P}" selected="true">trypsin - [KR]|{P}</option> + <option value="[FKLMRWY]__pc__{P}">trypsin/chymotrypsin - [FKLMRWY]|{P}</option> + <option value="[KR]__pc__{P},[M]__pc__{P}">trypsin/cnbr - [KR]|{P},[M]|{P}</option> + <option value="[DEKR]__pc__{P}">trypsin_gluc - [DEKR]|{P}</option> </param> - <param name="fragment_ion_tol" help="Fragment Ion Tolerance in Daltons" type="float" value="0.65" min="0" max="10000" label="Fragment ion tolerance"/> + <param name="fragment_ion_tol" help="Fragment Ion Tolerance in Daltons" type="float" value="0.5" min="0" max="10000" label="Fragment ion tolerance"/> - <param name="precursor_ion_tol" help="Precursor Ion Tolerance (Da or ppm)" type="float" value="100" min="0" max="10000" label="Precursor ion tolerance"/> + <param name="precursor_ion_tol" help="Precursor Ion Tolerance (Da or ppm)" type="float" value="10" min="0" max="10000" label="Precursor ion tolerance"/> <param name="precursor_tolu" type="select" format="text"> <label>Precursor Ion Tolerance Units</label> <option value="ppm">ppm</option> <option value="Da">Da</option> </param> - <param name="allow_multi_isotope_search" type="boolean" label="Allow multi-isotope search" help="This allows peptide candidates in windows around -1 Da and -2 Da from the acquired mass to be considered. Only applicable when the minus/plus window above is set to less than 0.5 Da. Good for accurate-mass instruments for which the reported precursor mass is not corrected to the monoisotopic mass." truevalue="" falsevalue=""/> + <param name="allow_multi_isotope_search" type="boolean" label="Allow multi-isotope search" help="This allows peptide candidates in windows around -1 Da and -2 Da from the acquired mass to be considered. Only applicable when the minus/plus window above is set to less than 0.5 Da. Good for accurate-mass instruments for which the reported precursor mass is not corrected to the monoisotopic mass." truevalue="--multi-isotope-search" falsevalue=""/> </inputs> @@ -187,7 +188,19 @@ <data format="tandem" name="output" metadata_source="input_file" label="X!Tandem_vs_${database.dbkey if $database.has_key('dbkey') else $database.fasta_file.display_name}.${input_file.display_name}.${input_file.display_name}.tandem"/> </outputs> - + <tests> + <!-- Just test that the tool runs and produces vaguely correct output --> + <test> + <param name="source_select" value="input_ref"/> + <param name="fasta_file" value="testdb.fasta" format="fasta"/> + <param name="input_file" value="tiny.mzML" format="mzml"/> + <output name="output" format="tandem"> + <assert_contents> + <has_text text="tandem-style" /> + </assert_contents> + </output> + </test> + </tests> <help> **What it does**