diff chira_map.xml @ 6:1d3be7700f70 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"

--- a/chira_map.xml	Thu Apr 16 13:39:15 2020 -0400
+++ b/chira_map.xml	Thu May 07 03:39:22 2020 -0400
@@ -8,15 +8,26 @@
         chira_map.py -b
         -a '$alignment.aligner'
         -i '$query'
-        -b
         #if str($alignment.aligner) == "bwa":
             -s '$alignment.stranded'
             -l1 '$alignment.seed_length1'
             -l2 '$alignment.seed_length2'
             -s1 '$alignment.align_score1'
             -s2 '$alignment.align_score2'
+            -ma1 '$alignment.match1'
+            -mm1 '$alignment.mismatch1'
+            -ma2 '$alignment.match2'
+            -mm2 '$alignment.mismatch2'
+            -go1 '$alignment.gapo1'
+            -ge1 '$alignment.gape1'
+            -go2 '$alignment.gapo2'
+            -ge2 '$alignment.gape2'
+            -h1 '$alignment.nhits1'
+            -h2 '$alignment.nhits2'
+
         #else if str($alignment.aligner) == "clan":
             -s2 '$alignment.align_score'
+            -co '$alignment.chimeric_overlap'
         #end if
         #if str($reference.ref_type) == "single":
             -f1 '$reference.ref_fasta'
@@ -24,7 +35,6 @@
             -f1 '$reference.ref_fasta1'
             -f2 '$reference.ref_fasta2'
         #end if
-        -co '$chimeric_overlap'
         -p "\${GALAXY_SLOTS:-4}"
         -o ./
 
@@ -66,24 +76,35 @@
                        help="Seed length for 1st mapping iteration. bwa-mem parameter -k"/>
                 <param name="seed_length2" type="integer" value="6" label="Seed length 2" min="1"
                       help="Seed length for 2nd mapping iteration. bwa-mem parameter -k"/>
-                <param name="align_score1" type="integer" value="18" label="Minimum alignmnet score 1" min="1"
-                      help="Minimum alignment score in 1st mapping iteration. It
-                                must be smaller than --align_score1 parameter. bwa-mem parameter '-T'"/>
-                <param name="align_score2" type="integer" value="10" label="Minimum alignmnet score 2" min="1"
-                      help="Minimum alignment score in 2nd mapping iteration. bwa-mem parameter '-T'"/>
+                <param name="align_score1" type="integer" value="18" min="1"
+                       label="Minimum alignmnet score for 1st mapping iteration" help="bwa-mem parameter '-T'"/>
+                <param name="align_score2" type="integer" value="10" min="1"
+                       label="Minimum alignmnet score for 2nd mapping iteration" help="bwa-mem parameter '-T'"/>
+                <param name="match1" type="integer" value="1" label="Matching score for 1st mapping iteration"/>
+                <param name="mismatch1" type="integer" value="4" label="Mismatch penalty for 1st mapping iteration"/>
+                <param name="match2" type="integer" value="1" label="Matching score for 2nd mapping iteration"/>
+                <param name="mismatch2" type="integer" value="7" label="Mismatch penalty for 2nd mapping iteration"/>
+                <param name="gapo1" type="integer" value="6" label="Gap opening penalty for 1st mapping iteration"/>
+                <param name="gape1" type="integer" value="1" label="Gap extension penalty for 1st mapping iteration"/>
+                <param name="gapo2" type="integer" value="100" label="Gap opening penalty for 2nd mapping iteration"/>
+                <param name="gape2" type="integer" value="100" label="Gap extension penalty for 2nd mapping iteration"/>
+                <param name="nhits1" type="integer" value="50"
+                       label="Maximum number of allowed multi hits per read in 1st iteration"/>
+                <param name="nhits2" type="integer" value="100"
+                       label="Maximum number of allowed multi hits per read in 2nd iteration"/>
             </when>
             <when value="clan">
                 <param name="align_score" type="integer" value="10" label="Minimum length for each fragment" min="1"
                       help="Minimu length of the read segment that needs to be mapped. clan_search parameter '-l'"/>
+                <param name="chimeric_overlap" type="integer" value="2" label=" Maximum number of bases allowed
+                            between the chimericsegments of a read"/>
             </when>
         </conditional>
-        <param name="chimeric_overlap" type="integer" value="2" label=" Maximum number of bases allowed
-                    between the chimericsegments of a read"/>
     </inputs>
 
     <outputs>
-        <data format="bed" name="mapped_bed" from_work_dir="mapped.bed" label="ChiRA aligned BED on ${on_string}"/>
-        <data format="fasta" name="unmapped_fasta" from_work_dir="short.unmapped.fa"
+        <data format="bed" name="mapped_bed" from_work_dir="sorted.bed" label="ChiRA aligned BED on ${on_string}"/>
+        <data format="fasta" name="unmapped_fasta" from_work_dir="unmapped.fasta"
               label="ChiRA unmapped FASTA on ${on_string}">
             <filter>alignment['aligner'] == "bwa"</filter>
         </data>