diff samtools_phase.xml @ 6:dd8305e4e58e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit a972815cbd43dea553b3c0e4ad548f35d0023228-dirty

--- a/samtools_phase.xml	Tue May 09 11:16:22 2017 -0400
+++ b/samtools_phase.xml	Sun Jul 28 14:49:27 2019 -0400
@@ -37,7 +37,7 @@
                 <param name="min_bq" argument="-Q" type="integer" value="13" label="Minimum base quality to be used in het calling" />
                 <param name="read_depth" argument="-D" type="integer" value="256" label="Read depth" />
                 <param name="ignore_chimeras" argument="-F" type="boolean" truevalue="-F" falsevalue="" checked="False" label="Do not attempt to fix chimeric reads" />
-                <param name="drop_ambiguous" argument="-A" type="boolean" truevalue="-A 1" falsevalue="" checked="False" label="Drop reads with ambiguous phase" />
+                <param name="drop_ambiguous" argument="-A" type="boolean" truevalue="-A" falsevalue="" checked="False" label="Drop reads with ambiguous phase" />
             </when>
         </conditional>
     </inputs>
@@ -45,7 +45,7 @@
         <data format="txt" name="phase_sets" />
         <data format="bam" from_work_dir="phase_wrapper.0.bam" name="phase0" label="${tool.name} on ${on_string}: Phase-0 reads" />
         <data format="bam" from_work_dir="phase_wrapper.1.bam" name="phase1" label="${tool.name} on ${on_string}: Phase-1 reads" />
-        <data format="bam" from_work_dir="phase_wrapper.chimeras.bam" name="chimera" label="${tool.name} on ${on_string}: Chimeric reads" />
+        <data format="bam" from_work_dir="phase_wrapper.chimera.bam" name="chimera" label="${tool.name} on ${on_string}: Chimeric reads" />
     </outputs>
     <tests>
         <test>
@@ -54,7 +54,7 @@
             <output name="phase_sets" file="samtools_phase_out_1_log.txt" ftype="txt" />
             <output name="phase0" file="samtools_phase_out_1_phase0.bam" ftype="bam" />
             <output name="phase1" file="samtools_phase_out_1_phase1.bam" ftype="bam" />
-            <output name="chimera" file="empty_file.bam" compare="contains" />
+            <output name="chimera" file="empty_file.bam" ftype="bam" />
         </test>
         <test>
             <param name="input_bam" value="samtools_phase_in_2.bam" /> 
@@ -68,7 +68,7 @@
             <output name="phase_sets" file="samtools_phase_out_2_log.txt" ftype="txt" />
             <output name="phase0" file="samtools_phase_out_2_phase0.bam" ftype="bam" />
             <output name="phase1" file="samtools_phase_out_2_phase1.bam" ftype="bam" />
-            <output name="chimera" file="empty_file.bam" compare="contains" />
+            <output name="chimera" file="samtools_phase_out_2_chimera.bam" />
         </test>
         <test>
             <param name="input_bam" value="samtools_phase_in_2.bam" /> 
@@ -82,7 +82,7 @@
             <output name="phase_sets" file="samtools_phase_out_3_log.txt" ftype="txt" />
             <output name="phase0" file="samtools_phase_out_3_phase0.bam" ftype="bam" />
             <output name="phase1" file="samtools_phase_out_3_phase1.bam" ftype="bam" />
-            <output name="chimera" file="empty_file.bam" compare="contains" />
+            <output name="chimera" file="empty_file.bam"/>
         </test>
     </tests>
     <help><![CDATA[