diff samtools_bam_to_cram.xml @ 4:7d3cd2087698 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 0f75269223c0821c6c82acf98fde947d0f816f2b"

--- a/samtools_bam_to_cram.xml	Thu Oct 17 02:16:13 2019 -0400
+++ b/samtools_bam_to_cram.xml	Tue Sep 28 16:10:21 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="samtools_bam_to_cram" name="samtools BAM to CRAM" version="@TOOL_VERSION@">
+<tool id="samtools_bam_to_cram" name="samtools BAM to CRAM" version="@TOOL_VERSION@" profile="@PROFILE@">
     <description>convert BAM alignments to CRAM format</description>
 
     <macros>
@@ -20,7 +20,7 @@
 
             -@ \$addthreads
 	    -C
-	    -h 
+	    -h
             -o '${output_alignment}'
             -T '$reffa'
             -t '$reffai'
@@ -34,23 +34,7 @@
 
     <inputs>
         <param name="input" type="data" format="bam,sam" label="BAM (or SAM) alignment file"/>
-        <conditional name="addref_cond">
-            <param name="addref_select" type="select" label="Load reference genome from">
-                <option value="cached">Local cache</option>
-                <option value="history">History</option>
-            </param>
-            <when value="cached">
-                <param name="ref" type="select" label="Reference genome">
-                    <options from_data_table="fasta_indexes">
-                        <filter type="data_meta" ref="input" key="dbkey" column="dbkey" />
-                    </options>
-                    <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
-                </param>
-            </when>
-            <when value="history">
-                <param name="ref" type="data" format="fasta" label="Reference FASTA file"/>
-            </when>
-        </conditional>
+        <expand macro="mandatory_reference" argument="-t"/>
         <conditional name="parameter_regions">
             <param name="target_region" type="select" label="Choose conversion within specific genomic region(s)">
                 <option value="entire_input_file">Entire BAM alignment file</option>
@@ -78,16 +62,14 @@
             <param name="addref_select" value="history" />
             <param name="ref" value="test.fa" />
             <param name="target_region" value="entire_input_file" />
-
-            <output name="output_alignment" file="test.cram" compare="sim_size" delta="250" />
+            <output name="output_alignment" file="test_bam.cram" ftype="cram" compare="sim_size" delta="250" />
         </test>
         <test>
             <param name="input" value="test.sam" ftype="sam" />
             <param name="addref_select" value="history" />
             <param name="ref" value="test.fa" />
             <param name="target_region" value="entire_input_file" />
-
-            <output name="output_alignment" file="test.cram" compare="sim_size" delta="250" />
+            <output name="output_alignment" file="test_sam.cram" ftype="cram" compare="sim_size" delta="250" />
         </test>
         <test>
             <param name="input" value="test.bam" ftype="bam" />
@@ -95,8 +77,7 @@
             <param name="ref" value="test.fa" />
             <param name="target_region" value="region" />
             <param name="region_string" value="CHROMOSOME_I" />
-
-            <output name="output_alignment" file="test.cram" compare="sim_size" delta="250" />
+            <output name="output_alignment" file="test_chr1.cram" ftype="cram" compare="sim_size" delta="250" />
         </test>
         <test>
             <param name="input" value="test.bam" ftype="bam" />
@@ -104,15 +85,14 @@
             <param name="ref" value="test.fa" />
             <param name="target_region" value="regions_bed_file" />
             <param name="regions_bed_file" value="test.bed" ftype="bed" />
-
-            <output name="output_alignment" file="test.cram" compare="sim_size" delta="250" />
+            <output name="output_alignment" file="test_regions.cram" ftype="cram" compare="sim_size" delta="250" />
         </test>
         <test>
             <param name="input" ftype="bam" dbkey="equCab2" value="sam_to_bam_out2.bam" />
             <param name="addref_select" value="cached" />
             <param name="ref" value="equCab2chrM" />
             <param name="target_region" value="entire_input_file" />
-            <output name="output_alignment" file="test2.cram" compare="sim_size" delta="250" />
+            <output name="output_alignment" file="test2.cram" ftype="cram" compare="sim_size" delta="250" />
         </test>
     </tests>