Mercurial > repos > iuc > chira_map
diff chira_map.xml @ 6:1d3be7700f70 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
author | iuc |
---|---|
date | Thu, 07 May 2020 03:39:22 -0400 |
parents | 39bb70c2764e |
children | 6b83059e8f34 |
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--- 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>