diff chira_merge.xml @ 8:c836a05bd6a3 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit d8a9a5bb648d24f3917951cd7862f449e4dd0688"

--- a/chira_merge.xml	Thu May 07 03:35:27 2020 -0400
+++ b/chira_merge.xml	Fri May 29 06:58:21 2020 -0400
@@ -11,6 +11,7 @@
             -g '$annotation.gtf'
         #end if
         -so '$segment_overlap'
+        -lt '$length_threshold'
         #if str($merge.mode) == "blockbuster":
             -bb
             -d '$merge.distance'
@@ -19,6 +20,7 @@
             -sc '$merge.scale'
         #else:
             -ao '$merge.alignment_overlap'
+            -ls '$merge.min_locus_size'
         #end if
         #if str($reference.ref_type) == "split":
             -f1 '$reference.ref_fasta1'
@@ -44,6 +46,8 @@
         </conditional>
         <param name="segment_overlap" type="float" value="0.7" label="Overlap fraction for merging mapped read positions to segments" min="0" max="1"
             help="Matching read positions with greater than this fraction overlap are merged into a segment"/>
+        <param name="length_threshold" type="float" value="0.9" label="Minimum length of the alignments as a fraction of longest" min="0" max="1"
+            help="Consider the alignments of a that read have at least longer than this value times the longest alignment for that read"/>
         <conditional name="merge">
             <param name="mode" type="select" label="Select the mode of merging">
                 <option value="overlap">Overlap based</option>
@@ -52,15 +56,17 @@
             <when value="overlap">
                 <param name="alignment_overlap" type="float" value="0.7" label="Overlap fraction for merging alignments" min="0" max="1"
                     help="Minimum fraction of BED entries that must overlap inorder to merge"/>
+                <param name="min_locus_size" type="integer" value="1" label="Minimum locus size"
+                            help="Minimum number of alignments to be present to output the merged a locus"/>
             </when>
             <when value="blockbuster">
                 <param name="distance" type="integer" value="30" label="Blockbuster parameter distance"
                     help="Minimum distance between two clusters"/>
-                <param name="min_cluster_height" type="float" value="10" label="Blockbuster parameter minClusterHeight"
+                <param name="min_cluster_height" type="integer" value="10" label="Blockbuster parameter minClusterHeight"
                     help="minimum height (readno) of a cluster"/>
-                <param name="min_block_height" type="float" value="1" label="Blockbuster parameter minBlockHeight"
+                <param name="min_block_height" type="integer" value="10" label="Blockbuster parameter minBlockHeight"
                     help="minimum height (readno) of a block"/>
-                <param name="scale" type="float" value="0.4" label="Blockbuster parameter scale" min="0" max="1"
+                <param name="scale" type="float" value="0.1" label="Blockbuster parameter scale" min="0" max="1"
                     help="scale stddev for a single read"/>
             </when>
         </conditional>
@@ -96,7 +102,7 @@
             <param name="ref_fasta2" value="ref2.fasta"/>
             <output name="segments_bed" >
                 <assert_contents>
-                    <has_text_matching expression="ENSMUST00000146006\t6703\t6718\t10\|2\|3,ENSMUST00000146006,6703,6718,\+,24S15M16S\t1\t\+" />
+                    <has_text_matching expression="ENSMUST00000037472\t672\t687\t2\|1\|4,ENSMUST00000037472,672,687,\+,14S15M25S\t1\t\+" />
                 </assert_contents>
             </output>
             <output name="merged_bed" >
@@ -133,6 +139,7 @@
             <param name="choice" value="yes" />
             <param name="gtf" value="annotation.gtf" />
             <param name="mode" value="blockbuster" />
+            <param name="min_block_height" value="1" />
             <param name="min_cluster_height" value="5" />
             <param name="ref_type" value="split"/>
             <param name="ref_fasta1" value="ref1.fasta"/>