# HG changeset patch
# User artbio
# Date 1504562101 14400
# Node ID da1aa7de2b195981802e356ff6ab3fbcf92589d3
# Parent  6b8adacd475094ef4dcdc90cdabcceb654284631
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit ddaf9622722487d010001cd1f255107adf0c332d

diff -r 6b8adacd4750 -r da1aa7de2b19 mircounts.py
--- a/mircounts.py	Wed Jul 26 19:15:08 2017 -0400
+++ b/mircounts.py	Mon Sep 04 17:55:01 2017 -0400
@@ -104,7 +104,6 @@
     writes a count table
     """
     F = open(outfile, 'w')
-    F.write('Gene\tCounts\n')
     for gene in sorted(countdict):
         F.write('%s\t%s\n' % (gene, str(countdict[gene])))
     F.close()
diff -r 6b8adacd4750 -r da1aa7de2b19 mircounts.xml
--- a/mircounts.xml	Wed Jul 26 19:15:08 2017 -0400
+++ b/mircounts.xml	Mon Sep 04 17:55:01 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="mircounts" name="miRcounts" version="0.9.3">
+<tool id="mircounts" name="miRcounts" version="0.9.4">
     <description> Counts miRNA alignments from small RNA sequence data</description>
     <requirements>
         <requirement type="package" version="1.18">gnu-wget</requirement>
@@ -9,7 +9,6 @@
         <requirement type="package" version="0.20_34=r3.3.2_0">r-lattice</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-        ## To be refactored with guidelines in https://github.com/ARTbio/tools-artbio/issues/140
         wget ftp://mirbase.org/pub/mirbase/CURRENT/genomes/${genomeKey}.gff3 && ## download gff3 specified by the variable genomeKey
         python '$__tool_directory__'/mature_mir_gff_translation.py --input ${genomeKey}.gff3 --output $gff3 && ## transcode the mature miR genome coordinates into coordinates relative to the corresponding "miRNA_primary_transcript".
         wget ftp://mirbase.org/pub/mirbase/CURRENT/hairpin.fa.gz &&
@@ -75,6 +74,48 @@
                 <column name="value" index="0"/>
             </options>
         </param>
+        <!-- work on proper selection of the url (that varies between gff, gff2 and gff3)
+        <param name="mirbase_version" type="select" label="Choose miRbase version">
+            <option selected="true" value="CURRENT">Current</option>
+            <option value="1.0">1.0</option>
+            <option value="1.1">1.1</option>
+            <option value="1.2">1.2</option>
+            <option value="1.3">1.3</option>
+            <option value="1.4">1.4</option>
+            <option value="1.5">1.5</option>
+            <option value="2.0">2.0</option>
+            <option value="2.1">2.0</option>
+            <option value="2.2">2.2</option>
+            <option value="3.0">3.0</option>
+            <option value="3.1">3.1</option>
+            <option value="4.0">4.0</option>
+            <option value="5.0">5.0</option>
+            <option value="5.1">5.1</option>
+            <option value="6.0">6.0</option>
+            <option value="7.0">7.0</option>
+            <option value="7.1">7.1</option>
+            <option value="8.0">8.0</option>
+            <option value="8.1">8.1</option>
+            <option value="8.2">8.2</option>
+            <option value="9.0">9.0</option>
+            <option value="9.1">9.1</option>
+            <option value="9.2">9.2</option>
+            <option value="10.0">10.0</option>
+            <option value="10.1">10.1</option>
+            <option value="11.0">11.0</option>
+            <option value="12.0">12.0</option>
+            <option value="13.0">13.0</option>
+            <option value="14">14</option>
+            <option value="15">15</option>
+            <option value="16">16</option>
+            <option value="17">17</option>
+            <option value="18">18</option>
+            <option value="19">19</option>
+            <option value="20">20</option>
+            <option value="21">21</option>
+            </options>
+        </param>
+        -->
         <param help="command [ bowtie -v 0,1,2,3 -M 1 --best --strata --norc ] will be used. Specify a value for -v (number of mismatches allowed)" label="Number of mismatches allowed" name="v" type="select">
             <option value="0">0</option>
             <option selected="true" value="1">1</option>
@@ -99,8 +140,16 @@
     <outputs>
         <data format="bam" label="BAM alignment" name="output" />
         <data format="gff3" label="GFF3 generated by miRCounts" name="gff3"/>
-        <data format="tabular" label="Pre-mir Counts" name="pre_mir_count_file" />
-        <data format="tabular" label="Mir Counts" name="mir_count_file" />
+        <data format="tabular" label="Pre-mir Counts" name="pre_mir_count_file">
+            <actions>
+                <action name="column_names" type="metadata" default="Gene,Counts" />
+            </actions>
+        </data>
+        <data format="tabular" label="Mir Counts" name="mir_count_file">
+            <actions>
+                <action name="column_names" type="metadata" default="Gene,Counts" />
+            </actions>
+        </data>
         <data format="tabular" label="Coverage Table" name="coverage_dataframe">
             <filter>plotting['plottingOption'] == "yes"</filter>
         </data>
diff -r 6b8adacd4750 -r da1aa7de2b19 test-data/mirs_clipped_count.tab
--- a/test-data/mirs_clipped_count.tab	Wed Jul 26 19:15:08 2017 -0400
+++ b/test-data/mirs_clipped_count.tab	Mon Sep 04 17:55:01 2017 -0400
@@ -1,4 +1,3 @@
-Gene	Counts
 dme-bantam-3p	8
 dme-bantam-5p	0
 dme-let-7-3p	0
diff -r 6b8adacd4750 -r da1aa7de2b19 test-data/mirs_unclipped_count.tab
--- a/test-data/mirs_unclipped_count.tab	Wed Jul 26 19:15:08 2017 -0400
+++ b/test-data/mirs_unclipped_count.tab	Mon Sep 04 17:55:01 2017 -0400
@@ -1,4 +1,3 @@
-Gene	Counts
 dme-bantam-3p	11
 dme-bantam-5p	0
 dme-let-7-3p	0
diff -r 6b8adacd4750 -r da1aa7de2b19 test-data/pre_mirs_clipped_count.tab
--- a/test-data/pre_mirs_clipped_count.tab	Wed Jul 26 19:15:08 2017 -0400
+++ b/test-data/pre_mirs_clipped_count.tab	Mon Sep 04 17:55:01 2017 -0400
@@ -1,4 +1,3 @@
-Gene	Counts
 dme-bantam	8
 dme-let-7	1
 dme-mir-1	217
diff -r 6b8adacd4750 -r da1aa7de2b19 test-data/pre_mirs_unclipped_count.tab
--- a/test-data/pre_mirs_unclipped_count.tab	Wed Jul 26 19:15:08 2017 -0400
+++ b/test-data/pre_mirs_unclipped_count.tab	Mon Sep 04 17:55:01 2017 -0400
@@ -1,4 +1,3 @@
-Gene	Counts
 dme-bantam	11
 dme-let-7	5
 dme-mir-1	483