Mercurial > repos > galaxyp > peptideshaker
changeset 32:ff592231f118 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
| author | galaxyp |
|---|---|
| date | Wed, 25 Jan 2017 15:37:43 -0500 |
| parents | f3f67aa3123b |
| children | bce45e9e6d70 |
| files | macros.xml peptide_shaker.xml searchgui.xml test-data/tiny_searchgui_result1.zip |
| diffstat | 4 files changed, 62 insertions(+), 30 deletions(-) [+] |
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--- a/macros.xml Wed Jan 18 16:43:44 2017 -0500 +++ b/macros.xml Wed Jan 25 15:37:43 2017 -0500 @@ -16,6 +16,8 @@ ### multiple enzymes? -enzyme "${enzyme}" ### -specificity + ### value per enzyme + -mc $missed_cleavages #set $fixed_mods_str = $fixed_modifications or '' #set $variable_mods_str = $variable_modifications or '' #if $fixed_mods_str @@ -26,10 +28,11 @@ #end if -min_charge $min_charge -max_charge $max_charge - ### value per enzyme - -mc $missed_cleavages -fi $forward_ion -ri $reverse_ion + -min_isotope ${min_isotope} + -max_isotope ${max_isotope} + </token> <token name="@SEARCHGUI_MAJOR_VERSION@">3</token> <token name="@SEARCHGUI_VERSION@">3.1.4</token> @@ -106,6 +109,8 @@ <option value="y" selected="true">y</option> <option value="z">z</option> </param> + <param name="min_isotope" label="Minimum precursor isotope" type="integer" value="0" help="default: 0" /> + <param name="max_isotope" label="Maximum precursor isotope" type="integer" value="1" help="default: 1" /> </xml> <xml name="citations">
--- a/peptide_shaker.xml Wed Jan 18 16:43:44 2017 -0500 +++ b/peptide_shaker.xml Wed Jan 25 15:37:43 2017 -0500 @@ -337,8 +337,12 @@ <param name="processing_options_selector" value="no"/> <param name="filtering_options_selector" value="no"/> <param name="outputs" value="zip,3"/> - <output name="output_zip" file="peptide_shaker_result1.zip" ftype="zip" compare="sim_size" delta="600" /> - <output name="output_psm" file="peptide_shaker_psm_result1.tabular" ftype="tabular" /> + <output name="output_zip" file="peptide_shaker_result1.zip" ftype="zip" compare="sim_size" delta="900" /> + <output name="output_psm"> + <assert_contents> + <has_text text="cds.comp41779_c0_seq1" /> + </assert_contents> + </output> </test> <test> <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_archive"/> @@ -346,14 +350,53 @@ <param name="filtering_options_selector" value="yes"/> <param name="min_peptide_length" value="1"/> <param name="outputs" value="0,1,2,3,4,5,6,7"/> - <output name="output_certificate" file="peptide_shaker_certificate_result2.txt" ftype="txt" lines_diff="6"/> - <output name="output_hierarchical" file="peptide_shaker_hierarchical_result2.tabular" ftype="tabular" /> - <output name="output_psm" file="peptide_shaker_psm_result2.tabular" ftype="tabular" /> - <output name="output_psm_phosphorylation" file="peptide_shaker_psm_phoshorylation_result2.tabular" ftype="tabular" /> - <output name="output_peptides" file="peptide_shaker_peptides_result2.tabular" ftype="tabular" /> - <output name="output_peptides_phosphorylation" file="peptide_shaker_peptides_phoshorylation_result2.tabular" ftype="tabular" /> - <output name="output_proteins" file="peptide_shaker_proteins_result2.tabular" ftype="tabular" /> - <output name="output_proteins_phosphorylation" file="peptide_shaker_proteins_phoshorylation_result2.tabular" ftype="tabular" /> + <output name="output_certificate"> + <assert_contents> + <has_text text="Tolerance: 100" /> + <has_text text="Carbamidomethylation of C" /> + </assert_contents> + </output> + <output name="output_hierarchical"> + <assert_contents> + <has_text_matching expression="1.1\tcds.comp41779_c0_seq1; cds.comp41779_c0_seq2" /> + </assert_contents> + </output> + <output name="output_psm"> + <assert_contents> + <not_has_text text="Phosphosite" /> + <has_text text="cds.comp41779_c0_seq1" /> + </assert_contents> + </output> + <output name="output_psm_phosphorylation"> + <assert_contents> + <has_text text="Phosphosite" /> + <has_text text="cds.comp41779_c0_seq1" /> + </assert_contents> + </output> + <output name="output_peptides"> + <assert_contents> + <has_text text="Modification" /> + <has_text text="cds.comp41779_c0_seq1" /> + </assert_contents> + </output> + <output name="output_peptides_phosphorylation"> + <assert_contents> + <has_text text="Phosphosite" /> + <has_text text="cds.comp41779_c0_seq1" /> + </assert_contents> + </output> + <output name="output_proteins"> + <assert_contents> + <has_text text="Modification" /> + <has_text text="cds.comp41779_c0_seq1" /> + </assert_contents> + </output> + <output name="output_proteins_phosphorylation"> + <assert_contents> + <has_text text="Phosphosite" /> + <has_text text="cds.comp41779_c0_seq1" /> + </assert_contents> + </output> </test> </tests> <help>
--- a/searchgui.xml Wed Jan 18 16:43:44 2017 -0500 +++ b/searchgui.xml Wed Jan 25 15:37:43 2017 -0500 @@ -1,4 +1,4 @@ -<tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@.0"> +<tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@.1"> <description> Perform protein identification using various search engines and prepare results for input to Peptide Shaker </description> @@ -101,9 +101,7 @@ -omssa_remove_prec ${omssa.remove_precursor} -omssa_scale_prec ${omssa.scale_precursor} -omssa_estimate_charge ${omssa.estimate_charge} - -omssa_memory ${omssa.omssa_memory} - ## -omssa_isotopes ${omssa.omssa_isotopes} -omssa_neutron ${omssa.omssa_neutron} -omssa_low_intensity "${omssa.omssa_low_intensity}" -omssa_high_intensity ${omssa.omssa_high_intensity} @@ -148,8 +146,6 @@ -msgf_protocol ${msgf.msgf_protocol} -msgf_num_matches ${msgf.msgf_num_matches} -msgf_additional ${msgf.msgf_additional} - -msgf_isotope_low ${msgf.msgf_isotope_low} - -msgf_isotope_high ${msgf.msgf_isotope_high} #end if #* Not working in tests @@ -168,8 +164,6 @@ -myrimatch_max_pep_length ${myrimatch.myrimatch_max_pep_length} -myrimatch_min_prec_mass ${myrimatch.myrimatch_min_prec_mass} -myrimatch_max_prec_mass ${myrimatch.myrimatch_max_prec_mass} - -myrimatch_isotope_low ${myrimatch.myrimatch_isotope_low} - -myrimatch_isotope_high ${myrimatch.myrimatch_isotope_high} -myrimatch_num_matches ${myrimatch.myrimatch_num_matches} -myrimatch_num_ptms ${myrimatch.myrimatch_num_ptms} -myrimatch_fragmentation ${myrimatch.myrimatch_fragmentation} @@ -581,9 +575,7 @@ <param name="omssa_memory" type="boolean" truevalue="1" falsevalue="0" checked="true" label="OMSSA: Map Sequences in Memory" help="Use memory mapped sequence libraries" /> - <!-- param name="omssa_isotopes" type="integer" value="0" - label="OMSSA: Number of Isotopes" help="Number of isotopes to use (integer), 0 implies monoisotopic (default)" / --> - <param name="omssa_neutron" type="float" value="1446.94" + <param name="omssa_neutron" type="float" value="1446.94" label="OMSSA: Neutron Mass" help="Mass after which OMSSA should consider neutron exact mass" /> <param name="omssa_low_intensity" type="float" value="0.0" label="OMSSA: Low Intensity Cutoff" help="Low intensity cutoff as a fraction of max peak" /> @@ -712,8 +704,6 @@ <option value="0" selected="True">output basic scores only</option> <option value="1" >output additional features</option> </param> - <param name="msgf_isotope_low" label="MSGF: Lower Isotope Error Range" type="integer" value="0" help="Lower isotope error range" /> - <param name="msgf_isotope_high" label="MSGF: Upper Isotope Error Range" type="integer" value="1" help="Upper isotope errror range" /> </when> </conditional> @@ -864,10 +854,6 @@ label="MyriMatch: Minimum Peptide Mass" help="Minimum 1+ mass of parent ion to be considered" /> <param name="myrimatch_max_prec_mass" type="float" value="10000.0" label="MyriMatch: Maximum Peptide Mass" help="Maximum 1+ mass of parent ion to be considered" /> - <param name="myrimatch_isotope_low" type="integer" value="-1" - label="MyriMatch: Lower Isotope Error Range" help="Lower isotope error ragne" /> - <param name="myrimatch_isotope_high" type="integer" value="2" - label="MyriMatch: Upper Isotope Error Range" help="Upper isotope error range" /> <param name="myrimatch_num_matches" type="integer" value="10" label="MyriMatch: Maximum Number of Spectrum Matches" help="Set the value for the maximum number of spectrum matches" /> <param name="myrimatch_num_ptms" type="integer" value="2" @@ -1099,7 +1085,6 @@ <param name="engines" value="X!Tandem,MSGF,MyriMatch,OMSSA,Comet"/> <param name="xtandem.xtandem_advanced" value="yes"/> <param name="xtandem_advanced.xtandem_refine_selector" value="yes"/> - <output name="output" file="tiny_searchgui_result1.zip" ftype="searchgui_archive" compare="sim_size" delta="30000" /> </test> <!-- Test that search works with MSAmanda --> @@ -1112,7 +1097,6 @@ <param name="min_charge" value="1"/> <param name="max_charge" value="3"/> <param name="engines" value="MS_Amanda"/> - <output name="output" file="tiny_searchgui_result_amandaonly.zip" ftype="searchgui_archive" compare="sim_size" delta="5000" /> </test> </tests>