Mercurial > repos > iuc > gemini_dump

changeset 2:a32c298053e4 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 11ee7ac206d41894c0b6a11f2439aaea490824f0
author iuc
date Thu, 09 Nov 2017 13:18:08 -0500
parents c3da7c5f2141
children 40f85b45e472
files gemini_dump.xml gemini_macros.xml repository_dependencies.xml tool_data_table_conf.xml.sample
diffstat 4 files changed, 17 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/gemini_dump.xml	Tue Mar 22 21:43:09 2016 -0400
+++ b/gemini_dump.xml	Thu Nov 09 13:18:08 2017 -0500
@@ -26,8 +26,8 @@
             <option value="--genotypes">All rows/columns from the variants table with one line per sample/genotype (--genotypes)</option>
             <option value="--samples">All rows/columns from the samples table (--samples)</option>
         </param>
-        <param argument="--header" type="boolean" label="Include a header of column names" truevalue="--header" falsevalue="" selected="False" />
-        <param argument="--tfam" type="boolean" label="Output sample information to TFAM information" truevalue="--tfam" falsevalue="" selected="False" />
+        <param argument="--header" type="boolean" label="Include a header of column names" truevalue="--header" falsevalue="" checked="False" />
+        <param argument="--tfam" type="boolean" label="Output sample information to TFAM information" truevalue="--tfam" falsevalue="" checked="False" />
     </inputs>
     <outputs>
         <data name="outfile" format="tabular" />
--- a/gemini_macros.xml	Tue Mar 22 21:43:09 2016 -0400
+++ b/gemini_macros.xml	Thu Nov 09 13:18:08 2017 -0500
@@ -3,6 +3,8 @@
         <requirements>
             <requirement type="package" version="0.18.1">gemini</requirement>
             <requirement type="package" version="0.2.6">tabix</requirement>
+            <!-- for conda useage -->
+            <!--requirement type="package" version="1.3.1">htslib</requirement-->
             <yield />
         </requirements>
     </xml>
@@ -63,6 +65,7 @@
                     <option value="impact_severity">impact_severity</option>
                     <option value="max_aaf_all">alternative allele frequency</option>
                 </param>
+                <param name="extra_cols" type="text" label="Additional columns." help="Separate by whitespace"/>
             </when>
         </conditional>
     </xml>
@@ -96,6 +99,16 @@
         #end if
     </token>
 
+    <token name="@COLUMN_SELECT@">
+        #if $report.report_selector != 'all':
+            --columns "${report.columns}
+            #if str($report.extra_cols).strip()
+                #echo ','+','.join(str($report.extra_cols).split()) 
+            #end if
+            "
+        #end if
+    </token>
+
     <xml name="family">
         <param name="families" type="text" value="" label="Comma seperated list of families to restrict the analysis to." help="e.g. Family1,Family3 (--families)"/>
     </xml>
--- a/repository_dependencies.xml	Tue Mar 22 21:43:09 2016 -0400
+++ b/repository_dependencies.xml	Thu Nov 09 13:18:08 2017 -0500
@@ -1,4 +1,4 @@
 <?xml version="1.0"?>
 <repositories description="This requires the GEMINI data manager definition to install all required annotation databases.">
-    <repository changeset_revision="345412d58d75" name="data_manager_gemini_database_downloader" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="172815da3d41" name="data_manager_gemini_database_downloader" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
 </repositories>
--- a/tool_data_table_conf.xml.sample	Tue Mar 22 21:43:09 2016 -0400
+++ b/tool_data_table_conf.xml.sample	Thu Nov 09 13:18:08 2017 -0500
@@ -1,5 +1,5 @@
 <tables>
-    <table name="gemini_databases" comment_char="#">
+    <table name="gemini_databases" comment_char="#" allow_duplicate_entries="False">
         <columns>value, dbkey, name, path</columns>
         <file path="tool-data/gemini_databases.loc" />
     </table>