Mercurial > repos > pieterlukasse > prims_workflows

changeset 1:4719f745bf02 default tip

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setting the correct dependencies to main toolshed
author pieter.lukasse@wur.nl
date Wed, 08 Jan 2014 16:38:32 +0100
parents b3ccb17adda3
children
files PRIMS_iTRAQ_labeled_data.ga
diffstat 1 files changed, 6 insertions(+), 6 deletions(-) [+]
line wrap: on
line diff
--- a/PRIMS_iTRAQ_labeled_data.ga	Wed Jan 08 11:44:26 2014 +0100
+++ b/PRIMS_iTRAQ_labeled_data.ga	Wed Jan 08 16:38:32 2014 +0100
@@ -98,7 +98,7 @@
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             "post_job_actions": {}, 
             "tool_errors": null, 
-            "tool_id": "testtoolshed.g2.bx.psu.edu/repos/pieterlukasse/prims_masscomb/masscomb_xtandem200/2.0.0", 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/pieterlukasse/prims_masscomb/masscomb_xtandem200/2.0.0", 
             "tool_state": "{\"__page__\": 0, \"fragment_error_units\": \"\\\"Daltons\\\"\", \"precursor_mass_tolerance_lower\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"database\": \"null\", \"minimum_fragment_mz\": \"\\\"150\\\"\", \"fileType\": \"{\\\"type\\\": \\\"fileSet\\\", \\\"__current_case__\\\": 1, \\\"inputFile\\\": null}\", \"potential_modifications\": \"[\\\"45.987721@C\\\", \\\"144.102063@[\\\", \\\"144.102063@K\\\"]\", \"cleavage_site\": \"\\\"[RK]|{P}\\\"\", \"maximum_missed_cleavage_sites\": \"\\\"1\\\"\", \"fixed_modifications\": \"\\\"45.987721@C,144.102063@[,144.102063@K\\\"\", \"refinementOpt\": \"{\\\"refinement\\\": \\\"yes\\\", \\\"refine_potential_modifications\\\": null, \\\"refine_max_valid_expect\\\": \\\"0.01\\\", \\\"__current_case__\\\": 0, \\\"refine_point_mutation\\\": \\\"yes\\\"}\", \"max_valid_expect\": \"\\\"0.1\\\"\", \"precursor_mass_tolerance_upper\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"fragment_mass_tolerance\": \"\\\"0.6\\\"\", \"precursor_error_units\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"reverse_scoring\": \"\\\"no\\\"\", \"chromInfo\": \"\\\"/home/lukas007/galaxy-test/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null}", 
             "tool_version": "2.0.0", 
             "type": "tool", 
@@ -127,7 +127,7 @@
             }, 
             "post_job_actions": {}, 
             "tool_errors": null, 
-            "tool_id": "testtoolshed.g2.bx.psu.edu/repos/pieterlukasse/prims_masscomb/masscomb_dbsearch_converter/1.0.1", 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/pieterlukasse/prims_masscomb/masscomb_dbsearch_converter/1.0.1", 
             "tool_state": "{\"__page__\": 0, \"fileType\": \"{\\\"inputFormatType\\\": {\\\"isMs2SpectrumIdStartingAtZero\\\": \\\"true\\\", \\\"inputFormat\\\": \\\"xtandem\\\", \\\"__current_case__\\\": 0, \\\"inputFile\\\": null}, \\\"type\\\": \\\"fileSet\\\", \\\"__current_case__\\\": 1}\", \"chromInfo\": \"\\\"/home/lukas007/galaxy-test/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null}", 
             "tool_version": "1.0.1", 
             "type": "tool", 
@@ -164,7 +164,7 @@
             }, 
             "post_job_actions": {}, 
             "tool_errors": null, 
-            "tool_id": "testtoolshed.g2.bx.psu.edu/repos/pieterlukasse/prims_proteomics/quantiline1/1.0.2", 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/pieterlukasse/prims_proteomics/quantiline1/1.0.2", 
             "tool_state": "{\"ppidsFileName\": \"null\", \"__page__\": 0, \"labelMzValues\": \"\\\"114.0,115.0,116.0,117.0\\\"\", \"__rerun_remap_job_id__\": null, \"spectraDataFile\": \"null\", \"chromInfo\": \"\\\"/home/lukas007/galaxy-test/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"labelmTol\": \"\\\"0.5\\\"\"}", 
             "tool_version": "1.0.2", 
             "type": "tool", 
@@ -221,7 +221,7 @@
             }, 
             "post_job_actions": {}, 
             "tool_errors": null, 
-            "tool_id": "testtoolshed.g2.bx.psu.edu/repos/pieterlukasse/prims_proteomics/msfilt/1.0.2", 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/pieterlukasse/prims_proteomics/msfilt/1.0.2", 
             "tool_state": "{\"annotationSourceFiles\": \"[{\\\"identificationsFile\\\": null, \\\"__index__\\\": 0, \\\"spectraFile\\\": null}]\", \"filterOutFPIds\": \"\\\"True\\\"\", \"filterOutFPAnnotations\": \"\\\"True\\\"\", \"addRawIntensityInfo\": \"\\\"False\\\"\", \"addScaledIntensityInfo\": \"\\\"False\\\"\", \"__page__\": 0, \"apmlFile\": \"null\", \"fpCriteriaExpression\": \"\\\"qmDRT <0 or qmDMA <-0.5 or (qmDMP <-0.5 and qmBSCR<-0.5) or (!isNaN(smXTD) and smXTD >0.01)\\\"\", \"statisticalMeasuresConfig\": \"\\\"smXTD => MS:1001330,XSLASH!Tandem:expect,min \\\\r\\\\npvCSVEX => p_value,CSV_EXPORT,min \\\\r\\\\nsmAUTO_LIKELIHOOD => AUTOMOD_LOGLIKELIHOOD,PLGS/Auto-mod,max \\\\r\\\\nsmLIKELIHOOD => LOGLIKELIHOOD,PLGS/Databank-search,max \\\"\", \"rankingWeightConfig\": \"\\\"qmDRT => delta rt (standard score),1 \\\\r\\\\nqmDMA => delta mass annotation (standard score),1 \\\\r\\\\nqmDMP => delta mass psm (standard score),1 \\\\r\\\\nqmBSCR => best peptide score (standard score),1 \\\\r\\\\nqmALCV => alignment coverage (fraction),1 \\\\r\\\\nqmSTCV => score type coverage (fraction),1 \\\\r\\\\nqmPACV => peptide's best proteinAnnotCoverage (standard score),1 \\\\r\\\\nqmPICV => peptide's best proteinIdentifCoverage (standard score),1 \\\\r\\\\nqmANS => annotation sources (count),1 \\\\r\\\\nqmCSEV => charge states evidence (count),0.2 \\\\r\\\\nqmBCSP=> best correlation with source or product peptide (correl),1 \\\\r\\\\nqmBCCS => best correlation with other charge state (correl),1 \\\\r\\\\nqmBCOS => best correlation with other sibling peptide (correl),1 \\\"\", \"addRawRankingInfo\": \"\\\"False\\\"\", \"fpCriteriaExpressionForIds\": \"\\\"(qmDMP <-0.5 and qmBSCR<-0.5) or (!isNaN(smXTD) and smXTD >0.01)\\\"\", \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/home/lukas007/galaxy-test/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"filterOutUnannotatedAlignments\": \"\\\"True\\\"\"}", 
             "tool_version": "1.0.2", 
             "type": "tool", 
@@ -266,7 +266,7 @@
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+            "tool_id": "toolshed.g2.bx.psu.edu/repos/pieterlukasse/prims_proteomics/quantifere1/1.0.2", 
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             "tool_version": "1.0.2", 
             "type": "tool", 
@@ -303,7 +303,7 @@
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+            "tool_id": "toolshed.g2.bx.psu.edu/repos/pieterlukasse/primv_visualization/cytoexport1/1.0.2", 
             "tool_state": "{\"__page__\": 0, \"csvDataFile\": \"null\", \"__rerun_remap_job_id__\": null, \"configInputMode\": \"{\\\"vizMapPropsFile\\\": \\\"/com/pri/cytoexport/resources/quantifere_network_layout.props\\\", \\\"type\\\": \\\"existingTemplate\\\", \\\"alternativeTableImportJsonFile\\\": \\\"/com/pri/cytoexport/resources/quantifere_network_config.json\\\", \\\"__current_case__\\\": 0}\", \"chromInfo\": \"\\\"/home/lukas007/galaxy-test/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"vizStyleName\": \"\\\"default\\\"\"}", 
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             "type": "tool",