changeset 1:e8cb43bd2fe4 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 61c83ac999a040604915ff7cf92670b2635b967e"

--- a/bacteria_tradis.xml	Wed Jan 29 15:40:42 2020 +0000
+++ b/bacteria_tradis.xml	Fri Feb 07 10:20:18 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="bacteria_tradis" name="Bio-TraDis reads to counts" version="@VERSION@">
+<tool id="bacteria_tradis" name="Bio-TraDis reads to counts" version="@TOOL_VERSION@+galaxy@VERSION@">
     <description></description>
     <macros>
           <import>macros.xml</import>
@@ -81,9 +81,9 @@
     </inputs>
     
     <outputs>
-        <data format="txt" name="Statistics" label="${input_fastq.name} Statistics​" from_work_dir="file.stats" />
-        <data name="Counts" format="tabular" from_work_dir="./*.gz" />
-        <data name="Aligned_reads" format="bam" from_work_dir="./*.bam" />
+        <data format="txt" name="Statistics" from_work_dir="file.stats" label="${tool.name} on ${on_string} : Statistics" />
+        <data name="Counts" format="tabular.gz" from_work_dir="./*.gz" label="${tool.name} on ${on_string} : Counts"  />
+        <data name="Aligned_reads" format="bam" from_work_dir="./*.bam" label="${tool.name} on ${on_string} : Mapped Reads"  />
     </outputs>
     
     <tests>
@@ -174,4 +174,3 @@
 
 
 
-

--- a/macros.xml	Wed Jan 29 15:40:42 2020 +0000
+++ b/macros.xml	Fri Feb 07 10:20:18 2020 +0000
@@ -1,9 +1,10 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@VERSION@">1</token>
+    <token name="@VERSION@">2</token>
+    <token name="@TOOL_VERSION@">1.4.5</token>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="1.4.5">biotradis</requirement>
+            <requirement type="package" version="@TOOL_VERSION@">biotradis</requirement>
         </requirements>
     </xml>
     <xml name="citations">

--- a/tradis_essentiality.xml	Wed Jan 29 15:40:42 2020 +0000
+++ b/tradis_essentiality.xml	Fri Feb 07 10:20:18 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="tradis_essentiality" name="Bio-TraDis Essentiality Predictions" version="@VERSION@">
+<tool id="tradis_essentiality" name="Bio-TraDis Essentiality Predictions" version="@TOOL_VERSION@+galaxy@VERSION@">
     <description></description>
     <macros>
           <import>macros.xml</import>
@@ -78,4 +78,3 @@
 
 
 
-

--- a/tradis_gene_insert_sites.xml	Wed Jan 29 15:40:42 2020 +0000
+++ b/tradis_gene_insert_sites.xml	Fri Feb 07 10:20:18 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="tradis_gene_insert_sites" name="Bio-TraDis counts to gene insertion data" version="@VERSION@">
+<tool id="tradis_gene_insert_sites" name="Bio-TraDis counts to gene insertion data" version="@TOOL_VERSION@+galaxy@VERSION@">
     <description></description>
     <macros>
           <import>macros.xml</import>
@@ -12,20 +12,20 @@
     
     <inputs>
         <param name="input_counts" type="data" format="tabular" label="Read counts" help="Read counts at each nucleotide position for both strands. The first column contains forward strand counts, and the second contains reverse strand counts."/>
-        <param name="input_annot" type="data" format="txt" label="EMBL file containing the reference genome annotations"/>
+        <param name="input_annot" type="data" format="embl" label="EMBL file containing the reference genome annotations"/>
        <param name="trim3" type="float" value="0.1" min="0" max="1" label="Portion of the gene to trim in 3' end'" help="Trim reads at the 3'end of genes. Some transposon insertions can be little disruptive when they occur end of genes. Trim to ignore these reads."/>
        <param name="trim5" type="float" value="0" min="0" max="1" label="Portion of the gene to trim" help="Trim reads at the 5'end of genes. Some transposon insertions can be little disruptive when they occur end of genes. Trim to ignore these reads."/>
        
     </inputs>
     
     <outputs>
-        <data name="gene_insert_sites" format="csv" from_work_dir="./*.csv"/>
+        <data name="gene_insert_sites" format="csv" from_work_dir="./*.csv" label="${tool.name} on ${on_string}"/>
     </outputs>
     
     <tests>
         <test>
             <param name="input_counts" ftype="tabular" value="tiny.out.gz.CP009273.1_60_120.insert_site_plot.gz"/>
-            <param name="input_annot" ftype="txt" value="tiny_ref.embl"/>
+            <param name="input_annot" ftype="embl" value="tiny_ref.embl"/>
             <param name="trim3" ftype="float" value="0"/>
             <param name="trim5" ftype="float" value="0"/>
             <output name="gene_insert_sites" file="tiny.out.gz.CP009273.1_60_120.tradis_gene_insert_sites.csv"  compare="sim_size" delta="200" />
@@ -73,4 +73,3 @@
 
 
 
-