Mercurial > repos > wolma > mimodd
comparison snap_caller.xml @ 6:85214e4428fd
upgrade to mimodd version 0.1.7.0
| author | Wolfgang Maier |
|---|---|
| date | Fri, 11 Sep 2015 16:25:49 +0200 |
| parents | bdd1995c9e66 |
| children | d79fe626c6fd |
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| 5:bdd1995c9e66 | 6:85214e4428fd |
|---|---|
| 1 <tool id="read_alignment" name="SNAP Read Alignment" version="0.1.6.1"> | 1 <tool id="read_alignment" name="SNAP Read Alignment" version="0.1.7.0"> |
| 2 <description>Map sequence reads to a reference genome using SNAP</description> | 2 <description>Map sequence reads to a reference genome using SNAP</description> |
| 3 <macros> | 3 <macros> |
| 4 <import>toolshed_macros.xml</import> | 4 <import>toolshed_macros.xml</import> |
| 5 </macros> | 5 </macros> |
| 6 <expand macro="requirements"/> | 6 <expand macro="requirements"/> |
| 16 #else: | 16 #else: |
| 17 '${i.mode_choose.input.ifile}' | 17 '${i.mode_choose.input.ifile}' |
| 18 #end if | 18 #end if |
| 19 --ofile '$outputfile' --iformat ${i.mode_choose.input.iformat} --oformat $oformat | 19 --ofile '$outputfile' --iformat ${i.mode_choose.input.iformat} --oformat $oformat |
| 20 --idx-seedsize '$set.seedsize' | 20 --idx-seedsize '$set.seedsize' |
| 21 --idx-slack '$set.slack' --maxseeds '$set.maxseeds' --maxhits '$set.maxhits' --clipping=$set.clipping --maxdist '$set.maxdist' --confdiff '$set.confdiff' --confadapt '$set.confadpt' | 21 --idx-slack '$set.slack' --maxseeds '$set.maxseeds' --maxhits '$set.maxhits' --clipping $set.clipping --maxdist '$set.maxdist' --confdiff '$set.confdiff' --confadapt '$set.confadpt' |
| 22 #if $i.mode_choose.input.header: | 22 #if $i.mode_choose.input.header: |
| 23 --header '${i.mode_choose.input.header}' | 23 --header '${i.mode_choose.input.header}' |
| 24 #end if | 24 #end if |
| 25 #if $str($i.mode_choose.mode) == "paired": | 25 #if $str($i.mode_choose.mode) == "paired": |
| 26 --spacing '$set.sp_min' '$set.sp_max' | 26 --spacing '$set.sp_min' '$set.sp_max' |
| 166 <param name="confdiff" type="integer" value="2" label="confidence threshold (default: 2)" help="Confidence threshold (SNAP option -c); the minimum edit distance difference between two alternate alignments required to reject the poorer alignment as suboptimal; higher values increase the rate of ambiguously aligned reads."/> | 166 <param name="confdiff" type="integer" value="2" label="confidence threshold (default: 2)" help="Confidence threshold (SNAP option -c); the minimum edit distance difference between two alternate alignments required to reject the poorer alignment as suboptimal; higher values increase the rate of ambiguously aligned reads."/> |
| 167 <param name="confadpt" type="integer" value="7" label="adaptive confdiff behaviour (default: 7)" help="Specifies how many seeds of a read may be ignored (based on the maximum hits value above) before the confidence threshold above gets increased by one for that read; helps fine-tuning alignment accuracy in repetitive regions of the genome."/> | 167 <param name="confadpt" type="integer" value="7" label="adaptive confdiff behaviour (default: 7)" help="Specifies how many seeds of a read may be ignored (based on the maximum hits value above) before the confidence threshold above gets increased by one for that read; helps fine-tuning alignment accuracy in repetitive regions of the genome."/> |
| 168 <param name="maxseeds" type="integer" value="25" label="maximum seeds per read (default: 25)" help="Number of seeds to use per read (SNAP option -n) when trying to match it to the reference genome; higher numbers will increase the rate of aligned reads and reduce the rate of misalignments, but will reduce performance."/> | 168 <param name="maxseeds" type="integer" value="25" label="maximum seeds per read (default: 25)" help="Number of seeds to use per read (SNAP option -n) when trying to match it to the reference genome; higher numbers will increase the rate of aligned reads and reduce the rate of misalignments, but will reduce performance."/> |
| 169 <param name="clipping" type="select" label="read clipping (default: from back and front)" help="Specifies from which end of a read low-quality bases should be clipped (SNAP option -Cxx)"> | 169 <param name="clipping" type="select" label="read clipping (default: from back and front)" help="Specifies from which end of a read low-quality bases should be clipped (SNAP option -Cxx)"> |
| 170 <option value="++">from back and front</option> | 170 <option value="++">from back and front</option> |
| 171 <option value="-+">from back only</option> | 171 <option value="x+">from back only</option> |
| 172 <option value="+-">from front only</option> | 172 <option value="+x">from front only</option> |
| 173 <option value="--">no clipping</option> | 173 <option value="xx">no clipping</option> |
| 174 </param> | 174 </param> |
| 175 <param name="selectivity" type="integer" value="1" label="selectivity (default: 1)" help="randomly choose 1/selectivity of the reads to score (SNAP option -S). The tool uses the default of 1 (or a 0 setting) to indicate that all reads should be worked with." /> | 175 <param name="selectivity" type="integer" value="1" label="selectivity (default: 1)" help="randomly choose 1/selectivity of the reads to score (SNAP option -S). The tool uses the default of 1 (or a 0 setting) to indicate that all reads should be worked with." /> |
| 176 <param name="filter_output" type="select" label="filter output (default: no filtering)" help="filter output (SNAP option -F for certain classes of reads."> | 176 <param name="filter_output" type="select" label="filter output (default: no filtering)" help="filter output (SNAP option -F for certain classes of reads."> |
| 177 <option value="off">no filtering</option> | 177 <option value="off">no filtering</option> |
| 178 <option value="a">aligned only</option> | 178 <option value="a">aligned only</option> |