Mercurial > repos > iuc > semibin_bin

changeset 1:4d561bdc2c31 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
author iuc
date Mon, 27 Mar 2023 08:24:46 +0000
parents 474701f91bcd
children dbf5571a8140
files bin.xml macros.xml
diffstat 2 files changed, 14 insertions(+), 9 deletions(-) [+]
line wrap: on
line diff
--- a/bin.xml	Fri Oct 14 21:48:47 2022 +0000
+++ b/bin.xml	Mon Mar 27 08:24:46 2023 +0000
@@ -57,7 +57,12 @@
             <filter>not no_recluster</filter>
             <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*).fa" format="fasta" directory="output/output_recluster_bins" />
         </collection>
-        <collection name="output_bins" type="list" label="${tool.name} on ${on_string}: Reconstructed bins before reclustering">
+        <collection name="output_prerecluster_bins" type="list" label="${tool.name} on ${on_string}: Reconstructed bins before reclustering">
+            <filter>not no_recluster</filter>
+            <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*).fa" format="fasta" directory="output/output_prerecluster_bins" />
+        </collection>
+        <collection name="output_bins" type="list" label="${tool.name} on ${on_string}: Reconstructed bins without reeclustering">
+            <filter>no_recluster</filter>
             <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*).fa" format="fasta" directory="output/output_bins" />
         </collection>
     </outputs>
@@ -83,7 +88,7 @@
             <param name="minfasta_kbs" value="200"/>
             <param name="no_recluster" value="false"/>
             <output_collection name="output_recluster_bins" count="0"/>
-            <output_collection name="output_bins" count="3">
+            <output_collection name="output_prerecluster_bins" count="3">
                 <element name="0" ftype="fasta">
                     <assert_contents>
                         <has_text text=">g1k_0"/>
@@ -162,4 +167,4 @@
 
     ]]></help>
     <expand macro="citations"/>
-</tool>
\ No newline at end of file
+</tool>
--- a/macros.xml	Fri Oct 14 21:48:47 2022 +0000
+++ b/macros.xml	Mon Mar 27 08:24:46 2023 +0000
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@TOOL_VERSION@">1.1.1</token>
+    <token name="@TOOL_VERSION@">1.5.1</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">21.01</token>
     <xml name="biotools">
@@ -282,7 +282,7 @@
         <data name="single_split_cov" format="csv" from_work_dir="output/*_data_split_cov.csv" label="${tool.name} on ${on_string}: Coverage (split data)">
             <filter>mode["select"]=="single" and extra_output and "coverage" in extra_output</filter>
         </data>
-        <collection name="co_cov" type="list" label="${tool.name} on ${on_string}: Coverage">
+        <collection name="co_cov" type="list" label="${tool.name} on ${on_string}: Coverage (co_cov)">
             <filter>mode["select"]=="co" and extra_output and "coverage" in extra_output</filter>
             <discover_datasets pattern=".*\.bam_(?P&lt;designation&gt;.*)_data_cov\.csv" format="csv" directory="output/" />
         </collection>
@@ -290,7 +290,7 @@
             <filter>mode["select"]=="co" and extra_output and "coverage" in extra_output</filter>
             <discover_datasets pattern=".*\.bam_(?P&lt;designation&gt;.*)_data_split_cov\.csv" format="csv" directory="output/" />
         </collection>
-        <collection name="multi_cov" type="list" label="${tool.name} on ${on_string}: Coverage">
+        <collection name="multi_cov" type="list" label="${tool.name} on ${on_string}: Coverage (multi_cov)">
             <filter>mode["select"]=="multi" and extra_output and "coverage" in extra_output</filter>
             <discover_datasets pattern=".*\.bam_(?P&lt;designation&gt;.*)_data_cov.csv" format="csv" directory="output/samples/" />
         </collection>
@@ -298,11 +298,11 @@
             <filter>mode["select"]=="multi" and extra_output and "coverage" in extra_output</filter>
             <discover_datasets pattern="(?P&lt;designation&gt;.*)\/data_cov.csv" format="csv" directory="output/samples/" recurse="true" match_relative_path="true"/>
         </collection>
-        <collection name="multi_split_cov" type="list" label="${tool.name} on ${on_string}: Coverage (split data) per sample">
+        <collection name="multi_split_cov" type="list" label="${tool.name} on ${on_string}: Coverage (split data) per sample (multi_split_cov)">
             <filter>mode["select"]=="multi" and extra_output and "coverage" in extra_output</filter>
             <discover_datasets pattern=".*\.bam_(?P&lt;designation&gt;.*)_data_split_cov.csv" format="csv" directory="output/samples/" />
         </collection>
-        <collection name="multi_split_cov_sample" type="list" label="${tool.name} on ${on_string}: Coverage (split data) per sample">
+        <collection name="multi_split_cov_sample" type="list" label="${tool.name} on ${on_string}: Coverage (split data) per sample (multi_split_cov_sample)">
             <filter>mode["select"]=="multi" and extra_output and "coverage" in extra_output</filter>
             <discover_datasets pattern="(?P&lt;designation&gt;.*)\/data_split_cov.csv" format="csv" directory="output/samples/" recurse="true" match_relative_path="true"/>
         </collection>
@@ -348,4 +348,4 @@
             <citation type="doi">10.1038/s41467-022-29843-y</citation>
         </citations>
     </xml>
-</macros>
\ No newline at end of file
+</macros>