Mercurial > repos > iuc > checkm_lineage_set

diff lineage_set.xml @ 0:b39999cdbf21 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
author: iuc
date: Fri, 29 Jul 2022 20:38:36 +0000
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lineage_set.xml	Fri Jul 29 20:38:36 2022 +0000
@@ -0,0 +1,61 @@
+<tool id="checkm_lineage_set" name="CheckM lineage_set" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>
+        Infer lineage-specific marker sets for each bin
+    </description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="biotools"/>
+    <expand macro="requirements"/>
+    <expand macro="version"/>
+    <command detect_errors="exit_code"><![CDATA[
+@HMM_MARKER_STATS_INPUTS@
+mkdir 'inputs/storage/tree' &&
+ln -s '$concatenated_tre' 'inputs/storage/tree/concatenated.tre' &&
+
+checkm lineage_set
+    'inputs'
+    '$marker'
+    --unique $unique
+    --multi $multi
+    $force_domain
+    $no_refinement
+    ]]></command>
+    <inputs>
+        <expand macro="hmm_marker_stats_inputs"/>
+        <param name="concatenated_tre" type="data" format="phyloxml" label="Concatenated tree" help="Output of the CheckM tree tool"/>
+        <expand macro="lineage_set_params" />
+    </inputs>
+    <outputs>
+        <expand macro="marker_output" />
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="phylo_hmm_info" ftype="zip" value="phylo_hmm_info.pkl.gz"/>
+            <param name="bin_stats_tree" ftype="tabular" value="bin_stats.tree.tsv"/>
+            <param name="hmmer_tree">
+                <collection type="list">
+                    <element name="637000110" ftype="txt" value="hmmer.tree.txt"/>
+                </collection>
+            </param>
+            <param name="concatenated_tre" ftype="phyloxml" value="concatenated.tre"/>
+            <param name="unique" value="10"/>
+            <param name="multi" value="10"/>
+            <param name="force_domain" value="false"/>
+            <param name="no_refinement" value="false"/>
+            <output name="marker" ftype="tabular">
+                <assert_contents>
+                    <has_text text="637000110"/>
+                    <has_text text="Lineage Marker File"/>
+                    <has_text text="PF00203"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+@HELP_HEADER@
+
+This command places bins in the genome tree.
+    ]]></help>
+    <expand macro="citations"/>
+</tool>