Mercurial > repos > thanhlv > bin3c

changeset 14:8d920f67589d draft

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planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit fd6117dcead9ad542ed6afd526adab8d1200fbcf-dirty
author thanhlv
date Mon, 14 Oct 2019 08:49:53 -0400
parents f3135aeac82c
children e0c0decc7ec0
files cluster.xml mkmap.xml
diffstat 2 files changed, 15 insertions(+), 11 deletions(-) [+]
line wrap: on
line diff
--- a/cluster.xml	Thu Oct 03 09:48:23 2019 -0400
+++ b/cluster.xml	Mon Oct 14 08:49:53 2019 -0400
@@ -7,12 +7,12 @@
     <expand macro="version_command" />
     <command detect_errors="exit_code"><![CDATA[
         bin3C cluster
-        $clobber
         --max-image $max_image
         --min-extent $min_extent
         --min-reflen $min_reflen
         --min-signal $min_signal
         -s 201987356473
+        --assembler $assembler
         $no_report
         $no_spades
         $no_plot
@@ -20,11 +20,15 @@
         $only_large
         $fasta
         $contact_map out
-    ]]></command>
-    
+    ]]>    </command>
+
     <inputs>
         <param name="contact_map" type="data" format="tar.gz" label="Contact map" help="This file is generated from mkmap command" />
-        <param name="clobber" type="boolean" truevalue="--clobber" falsevalue="" label="Clobber existing files" />
+        <param name="assembler" label="Assembly software used to create contigs" name="mode" type="select">
+            <option selected="true"  value="generic">generic</option>
+            <option value="megahit">megahit</option>
+            <option value="spades">spades</option>
+        </param>
         <param name="max_image" type="integer" min="1" value="4000" label="Maximum image size for plots"/>
         <param name="min_extent" type="integer" min="1" value="50000" label="Minimum cluster extent used in output"/>
         <param name="min_reflen" type="integer" min="1" value="1000" label="Minimum acceptable reference length"/>
@@ -45,7 +49,7 @@
         <data name="clustering_csv" format="tabular" label="{tool.name} on ${on_string} A per-cluster report of various statistics" from_work_dir="out/cluster_report.csv"/>
         <data name="cm_graph_edges" format="binary" label="{tool.name} on ${on_string} The graph used in clustering in edge list format" from_work_dir="out/cm_graph.edges"/>
         <data name="cm_graph_tree" format="text" label="{tool.name} on ${on_string} Infomap clustering output" from_work_dir="out/cm_graph.tree"/>
-        <data name="fasta" format="fasta" label="{tool.name} on ${on_string} Per-cluster multi-fasta sequences" from_work_dir="out/infomap.log"/> 
+        <data name="fasta" format="fasta" label="{tool.name} on ${on_string} Per-cluster multi-fasta sequences" from_work_dir="out/infomap.log"/>
     </outputs>
 
     <tests>
@@ -56,6 +60,6 @@
 
     Documentation can be found at `<https://github.com/cerebis/bin3C>`_.
 
-    ]]></help>
-<expand macro="citations" />
+    ]]>    </help>
+    <expand macro="citations" />
 </tool>
--- a/mkmap.xml	Thu Oct 03 09:48:23 2019 -0400
+++ b/mkmap.xml	Mon Oct 14 08:49:53 2019 -0400
@@ -7,15 +7,16 @@
     <expand macro="version_command" />
     <command detect_errors="exit_code"><![CDATA[
         bin3C mkmap
-        $clobber
         --max-image $max_image
         --min-extent $min_extent
         --min-reflen $min_reflen
         --min-signal $min_signal
-        $eta
-        --bin-size $bin_size
+        #if str($bin_size) != "0":
+            --bin-size $bin_size
+        #end if
         --min-insert $min_insert
         --min-mapq $min_mapq
+        $eta
         --strong $strong
         #if str($neb_name) != "":
             #for $enzyme in str($neb_name).split(',')
@@ -28,7 +29,6 @@
     <inputs>
         <param name="ref" type="data" format="fasta,fastaq.gz" label="Reference fasta sequence" />
         <param name="bam" type="data" format="bam" label="Input bam file in query order" />
-        <param name="clobber" type="boolean" truevalue="--clobber" falsevalue="" checked="false" label="Clobber existing files" />
         <param name="max_image" type="integer" min="1" value="4000" label="Maximum image size for plots"/>
         <param name="min_extent" type="integer" min="1" value="50000" label="Minimum cluster extent used in output"/>
         <param name="min_reflen" type="integer" min="1" value="1000" label="Minimum acceptable reference length"/>