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changeset 6:65b285f9f7ad draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit f7c987a36f3604b735bd0b288630045a05e0bc4d-dirty
author jorritb
date Fri, 19 May 2017 08:40:46 -0400
parents 44e32e51ff94
children
files nested_collection.xml roadmap
diffstat 2 files changed, 12 insertions(+), 8 deletions(-) [+]
line wrap: on
line diff
--- a/nested_collection.xml	Fri Apr 28 05:33:47 2017 -0400
+++ b/nested_collection.xml	Fri May 19 08:40:46 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="batched_set_list_creator" name="Create nested list" version="3.2">
+<tool id="batched_set_list_creator" name="Create nested list" version="3.3">
     <description>based on filenames and batch sizes</description>
     <stdio>
         <exit_code range="1:" />
@@ -38,15 +38,15 @@
     <outputs>
         <collection name="batched_fractions_mzid" type="list:list" label="Pooled batched mzIdentML data">
           <filter>filetype == "mzid"</filter>
-          <discover_datasets pattern="(?P&lt;identifier_0&gt;\w+[^_][^_][^_])___(?P&lt;identifier_1&gt;[\w.]+)\.data" ext="mzid" visible="false" />
+          <discover_datasets pattern="(?P&lt;identifier_0&gt;\w+[^_][^_][^_])___(?P&lt;identifier_1&gt;[\w.-]+)\.data" ext="mzid" visible="false" />
         </collection>
         <collection name="batched_fractions_perco" type="list:list" label="Pooled batched percolator data">
           <filter>filetype == "percout"</filter>
-          <discover_datasets pattern="(?P&lt;identifier_0&gt;\w+[^_][^_][^_])___(?P&lt;identifier_1&gt;[\w.]+)\.data" ext="percout" visible="false" />
+          <discover_datasets pattern="(?P&lt;identifier_0&gt;\w+[^_][^_][^_])___(?P&lt;identifier_1&gt;[\w.-]+)\.data" ext="percout" visible="false" />
         </collection>
         <collection name="batched_fractions_tab" type="list:list" label="Pooled batched tabular data">
           <filter>filetype == "tabular"</filter>
-          <discover_datasets pattern="(?P&lt;identifier_0&gt;\w+[^_][^_][^_])___(?P&lt;identifier_1&gt;[\w.]+)\.data" ext="tabular" visible="false" />
+          <discover_datasets pattern="(?P&lt;identifier_0&gt;\w+[^_][^_][^_])___(?P&lt;identifier_1&gt;[\w.-]+)\.data" ext="tabular" visible="false" />
         </collection>
     </outputs>
     <tests>
@@ -55,7 +55,7 @@
             <param name="filetype" value="mzid" />
             <param name="listtobatch">
                 <collection type="list">
-                    <element name="fraction_one_spectra" value="empty_file1.mzid"/>
+                    <element name="fraction_one_spectra.mzML" value="empty_file1.mzid"/>
                     <element name="fraction_two_spectra" value="empty_file2.mzid"/>
                     <element name="fraction_three_spectra" value="empty_file3.mzid"/>
                     <element name="fraction_four_spectra" value="empty_file4.mzid"/>
@@ -70,7 +70,7 @@
             </param>
             <output_collection name="batched_fractions_mzid" type="list:list">
                 <element name="pool0_batch0">
-                    <element name="inputfn00_fraction_one_spectra" ftype="mzid" file="empty_file1.mzid"/>
+                    <element name="inputfn00_fraction_one_spectra.mzML" ftype="mzid" file="empty_file1.mzid"/>
                     <element name="inputfn01_fraction_two_spectra" ftype="mzid" file="empty_file2.mzid"/>
                     <element name="inputfn02_fraction_three_spectra" ftype="mzid" file="empty_file3.mzid"/>
                     <element name="inputfn03_fraction_four_spectra" ftype="mzid" file="empty_file4.mzid"/>
@@ -96,7 +96,7 @@
             <param name="filetype" value="tabular" />
             <param name="listtobatch">
                 <collection type="list">
-                    <element name="fr_one_set1_spectra" value="empty_file1.mzid"/>
+                    <element name="fr_one_set1-spectra" value="empty_file1.mzid"/>
                     <element name="fr_two_set1_spectra" value="empty_file2.mzid"/>
                     <element name="fr_three_set1_spectra" value="empty_file3.mzid"/>
                     <element name="fr_four_set1_spectra" value="empty_file4.mzid"/>
@@ -114,7 +114,7 @@
             </param>
             <output_collection name="batched_fractions_tab" type="list:list">
                 <element name="set1_batch0">
-                    <element name="inputfn00_fr_one_set1_spectra" ftype="tabular" file="empty_file1.mzid"/>
+                    <element name="inputfn00_fr_one_set1-spectra" ftype="tabular" file="empty_file1.mzid"/>
                     <element name="inputfn01_fr_two_set1_spectra" ftype="tabular" file="empty_file2.mzid"/>
                     <element name="inputfn02_fr_three_set1_spectra" ftype="tabular" file="empty_file3.mzid"/>
                     <element name="inputfn03_fr_four_set1_spectra" ftype="tabular" file="empty_file4.mzid"/>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/roadmap	Fri May 19 08:40:46 2017 -0400
@@ -0,0 +1,4 @@
+- version bump
+- tandem2pin, sqt2pin
+- qvality
+- remove pout datatype, can be a subclass