Mercurial > repos > iuc > biom_convert

changeset 9:e177a8ea0bf1 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 4d77c1e4bd9f6876ee338858a8cd4c7e9528d54c
author iuc
date Wed, 13 Sep 2023 18:53:51 +0000
parents 72ed72122deb
children a4db66553a61
files biom_convert.xml macros.xml
diffstat 2 files changed, 12 insertions(+), 12 deletions(-) [+]
line wrap: on
line diff
--- a/biom_convert.xml	Sat Jan 21 11:17:10 2023 +0000
+++ b/biom_convert.xml	Wed Sep 13 18:53:51 2023 +0000
@@ -56,8 +56,8 @@
                 <option value="biom">BIOM File</option>
             </param>
             <when value="tsv">
-                <param name="input_fp" argument="--input-fp" type="data" format="tabular" label="Input table" />
-                <param name="process_obs_metadata" argument="--process-obs-metadata" type="select" label="Process metadata associated with observations when converting">
+                <param argument="--input-fp" type="data" format="tabular" label="Input table" />
+                <param argument="--process-obs-metadata" type="select" label="Process metadata associated with observations when converting">
                     <option value="" selected="True">Do Not process metadata</option>
                     <option value="taxonomy">taxonomy</option>
                     <option value="naive">naive</option>
@@ -65,7 +65,7 @@
                 </param>
             </when>
             <when value="biom">
-                <param name="input_fp" argument="--input-fp" type="data" format="biom1" label="Input BIOM table"/>
+                <param argument="--input-fp" type="data" format="biom1" label="Input BIOM table"/>
             </when>
         </conditional>
         <conditional name="output">
@@ -74,15 +74,15 @@
                 <option value="biom" selected="True">BIOM</option>
             </param>
             <when value="tsv">
-                <param name="header_key" argument="--header-key" type="text" value="" label="observation metadata to include" help="Leave empty to ignore" />
-                <param name="output_metadata_id" argument="--output-metadata-id" type="text" value="" label="name to be given to the observation metadata column" help="Leave empty to ignore" />
-                <param name="tsv_metadata_formatter" argument="--tsv-metadata-formatter" type="select" label="Method for formatting the observation metadata" >
+                <param argument="--header-key" type="text" value="" label="observation metadata to include" help="Leave empty to ignore" />
+                <param argument="--output-metadata-id" type="text" value="" label="name to be given to the observation metadata column" help="Leave empty to ignore" />
+                <param argument="--tsv-metadata-formatter" type="select" label="Method for formatting the observation metadata" >
                     <option value="naive" selected="True">naive</option>
                     <option value="sc_separated">Semi-colon separated</option>
                 </param>
             </when>
             <when value="biom">
-                <param name="table_type" argument="--table-type" type="select" label="Table Type" >
+                <param argument="--table-type" type="select" label="Table Type" >
                     <option value="OTU table">OTU table</option>
                     <option value="Pathway table">Pathway table</option>
                     <option value="Function table">Function table</option>
@@ -100,12 +100,12 @@
                     <when value="json">
                     </when>
                     <when value="hdf5">
-                        <param name="collapsed_observations" argument="--collapsed-observations" type="boolean" truevalue="" falsevalue="--collapsed-samples" checked="False" label="Use collapsed samples"/>
-                        <param name="collapsed_samples" argument="--collapsed-samples" type="boolean" truevalue="" falsevalue="--collapsed-samples" checked="False" label="Use collapsed observations"/>
+                        <param argument="--collapsed-observations" type="boolean" truevalue="--collapsed-observations" falsevalue="" checked="False" label="Use collapsed observations"/>
+                        <param argument="--collapsed-samples" type="boolean" truevalue="--collapsed-samples" falsevalue="" checked="False" label="Use collapsed samples"/>
                     </when>
                 </conditional>
-                <param name="sample_metadata_fp" argument="--sample-metadata-fp" type="data" format="tabular" optional="True" label="Add sample metadata from metadata mapping file" />
-                <param name="observation_metadata_fp" argument="--observation-metadata-fp" type="data" format="tabular" optional="True" label="Add observation metadata from mapping file" />
+                <param argument="--sample-metadata-fp" type="data" format="tabular" optional="True" label="Add sample metadata from metadata mapping file" />
+                <param argument="--observation-metadata-fp" type="data" format="tabular" optional="True" label="Add observation metadata from mapping file" />
             </when>
         </conditional>
     </inputs>
--- a/macros.xml	Sat Jan 21 11:17:10 2023 +0000
+++ b/macros.xml	Wed Sep 13 18:53:51 2023 +0000
@@ -6,7 +6,7 @@
         </requirements>
     </xml>
     <token name="@TOOL_VERSION@">2.1.14</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <token name="@PROFILE@">21.05</token>
     <xml name="version_command">
         <version_command>biom --version</version_command>