diff featurecounts.xml @ 7:3ce1c701b0df draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit a705dfd329f2e917d549215715385f5ef5001d17

--- a/featurecounts.xml	Thu Oct 26 15:11:19 2017 -0400
+++ b/featurecounts.xml	Mon Oct 30 14:49:13 2017 -0400
@@ -30,7 +30,9 @@
 
                 $extended_parameters.exon_exon_junction_read_counting_enabled.count_exon_exon_junction_reads
                 #if str($extended_parameters.exon_exon_junction_read_counting_enabled.count_exon_exon_junction_reads) == "-J"
-                    -G '$extended_parameters.exon_exon_junction_read_counting_enabled.genome'
+                    #if $extended_parameters.exon_exon_junction_read_counting_enabled.genome
+                        -G '$extended_parameters.exon_exon_junction_read_counting_enabled.genome'
+                    #end if
                 #end if
 
                 $extended_parameters.long_reads
@@ -274,8 +276,8 @@
                        label="Exon-exon junctions"
                        help="If specified, reads supporting each exon-exon junction will be counted" />
                 <when value="-J">
-                    <param name="genome" argument="-G" type="data" format="fasta"
-                           label="Reference sequence (genome) file"
+                    <param name="genome" argument="-G" type="data" format="fasta" optional="true"
+                           label="Reference sequence file"
                            help="The FASTA-format file that contains the reference sequences used in read mapping can be used to improve read counting for junctions" />
                 </when>
                 <when value="" />
@@ -397,25 +399,31 @@
 
         <data name="output_jcounts" format="tabular"
               label="${tool.name} on ${on_string}: junction counts">
-            <filter>extended_parameters.exon_exon_junction_read_counting_enabled.count_exon_exon_junction_reads == " -J"</filter>
+            <filter>extended_parameters['exon_exon_junction_read_counting_enabled']['count_exon_exon_junction_reads']</filter>
             <actions>
                 <action name="column_names" type="metadata" default="PrimaryGene,SecondaryGene,Site1_chr,Site1_location,Site1_strand,Site2_chr,Site2_location,Site2_strand,${alignment.name}" />
             </actions>
         </data>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="4">
             <param name="alignment" value="featureCounts_input1.bam" ftype="bam" />
             <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" />
             <param name="format" value="tabdel_short" />
             <param name="include_feature_length_file" value="true"/>
             <param name="ref_source" value="history" />
+            <param name="count_exon_exon_junction_reads" value="-J"/>
             <output name="output_short" file="output_1_short.tab">
                 <metadata name="column_names" value="Geneid,featureCounts_input1.bam"/>
             </output>
-            <output name="output_summary" file="output_1_summary.tab"/>
+            <output name="output_summary" file="output_1_summary.tab">
+                <metadata name="column_names" value="Status,featureCounts_input1.bam"/>
+            </output>
+            <output name="output_jcounts" file="output_1_jcounts.tab">
+                <metadata name="column_names" value="PrimaryGene,SecondaryGene,Site1_chr,Site1_location,Site1_strand,Site2_chr,Site2_location,Site2_strand,featureCounts_input1.bam"/>
+            </output>
         </test>
-        <test>
+        <test expect_num_outputs="3">
             <param name="alignment" value="featureCounts_input1.bam" ftype="bam" />
             <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" />
             <param name="format" value="tabdel_medium" />
@@ -428,7 +436,7 @@
                 <metadata name="column_names" value="Status,featureCounts_input1.bam"/>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="3">
             <param name="alignment" value="featureCounts_input1.bam" ftype="bam" />
             <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" />
             <param name="format" value="tabdel_full" />
@@ -445,48 +453,6 @@
             </output>
         </test>
         
-        <test>
-            <param name="alignment" value="featureCounts_input1.bam" ftype="bam" />
-            <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" />
-            <param name="format" value="tabdel_short" />
-            <param name="include_feature_length_file" value="true"/>
-            <param name="ref_source" value="history" />
-            <output name="output_short" file="output_2_short.tab">
-                <metadata name="column_names" value="Geneid,featureCounts_input1.bam"/>
-            </output>
-            <output name="output_summary" file="output_2_summary.tab">
-                <metadata name="column_names" value="Status,featureCounts_input1.bam"/>
-            </output>
-        </test>
-        <test>
-            <param name="alignment" value="featureCounts_input1.bam" ftype="bam" />
-            <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" />
-            <param name="format" value="tabdel_medium" />
-            <param name="include_feature_length_file" value="true"/>
-            <param name="ref_source" value="history" />
-            <output name="output_medium" file="output_2_medium.tab">
-                <metadata name="column_names" value="Geneid,featureCounts_input1.bam,Length"/>
-            </output>
-            <output name="output_summary" file="output_2_summary.tab">
-                <metadata name="column_names" value="Status,featureCounts_input1.bam"/>
-            </output>
-        </test>
-        <test>
-            <param name="alignment" value="featureCounts_input1.bam" ftype="bam" />
-            <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" />
-            <param name="format" value="tabdel_full" />
-            <param name="include_feature_length_file" value="true"/>
-            <param name="ref_source" value="history" />
-            <output name="output_full" file="output_2_full.tab">
-                <metadata name="column_names" value="Geneid,Chr,Start,End,Strand,Length,featureCounts_input1.bam"/>
-            </output>
-            <output name="output_summary" file="output_2_summary.tab">
-                <metadata name="column_names" value="Status,featureCounts_input1.bam"/>
-            </output>
-            <output name="output_feature_lengths" file="output_feature_lengths.tab">
-                <metadata name="column_names" value="Feature,Length"/>
-            </output>
-        </test>
     </tests>
     
     <help><![CDATA[