Mercurial > repos > jasper > pathoscope_map
comparison PathoMap.xml @ 0:94d7100ad5d0 draft default tip
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| author | jasper |
|---|---|
| date | Sat, 22 Apr 2017 23:47:18 -0400 |
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| -1:000000000000 | 0:94d7100ad5d0 |
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| 1 <tool id="pathoscope_map" name="Pathoscope Map" version="0.1.0"> | |
| 2 <description> Pathoscope Map </description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="2.0.6"> pathoscope </requirement> | |
| 5 </requirements> | |
| 6 <command> <![CDATA[ | |
| 7 #from os import listdir | |
| 8 #set path=$targetIndexPrefixes.fields.path.split(',')[0] | |
| 9 #set prefixes=[f for f in listdir(path) if f.endswith(".3.bt2")] | |
| 10 #set targetRefs=str($targetIndexPrefixes) | |
| 11 #set targetR=targetRefs.split(',') | |
| 12 #set p=[] | |
| 13 #for $f in prefixes | |
| 14 #for $t in targetR | |
| 15 #if $t in f | |
| 16 #set p = p + [f[:-6]] | |
| 17 #end if | |
| 18 #end for | |
| 19 #end for | |
| 20 #set target=','.join(p) | |
| 21 pathoscope MAP | |
| 22 #if str($reads.type) == "single" | |
| 23 -U $fastqU | |
| 24 #elif str($reads.type) == "paired" | |
| 25 -1 $fastq1 | |
| 26 -2 $fastq2 | |
| 27 #end if | |
| 28 -indexDir $path | |
| 29 -targetIndexPrefixes $target | |
| 30 -filterIndexPrefixes $filterIndexPrefixes 2>&1 | |
| 31 && mv outalign.sam "$outalign" | |
| 32 && mv pathomap-appendAlign.fq "$pathomap_appendAlign" | |
| 33 ]]> | |
| 34 </command> | |
| 35 <inputs> | |
| 36 <conditional name="reads"> | |
| 37 <param name="type" type="select" label="Is this single or paired reads" help=""> | |
| 38 <option value="single">Single-end</option> | |
| 39 <option value="paired">Paired-end</option> | |
| 40 </param> | |
| 41 <when value="single"> | |
| 42 <param name="fastqU" format="fastqsanger" type="data" label="FASTQ file" help="Input Read Fastq File (Unpaired/Single-end)" /> | |
| 43 </when> | |
| 44 <when value="paired"> | |
| 45 <param name="fastq1" format="fastqsanger" type="data" label="FASTQ file" help="Input Read Fastq File (Unpaired/Single-end)" /> | |
| 46 <param name="fastq2" format="fastqsanger" type="data" label="FASTQ file" help="Input Read Fastq File (Unpaired/Single-end)" /> | |
| 47 </when> | |
| 48 </conditional> | |
| 49 <param name="targetIndexPrefixes" multiple="true" type="select" label="targetIndexPrefixes" help="Target Index Prefixes"> | |
| 50 <options from_data_table="pathoscope_indexes"> | |
| 51 <filter type="sort_by" column="2"/> | |
| 52 <validator type="no_options" message="No indexes are available for the selected input dataset"/> | |
| 53 </options> | |
| 54 </param> | |
| 55 <param name="filterIndexPrefixes" multiple="true" type="select" label="filterIndexPrefixes" help="Filter Index Prefixes"> | |
| 56 <options from_data_table="pathoscope_indexes"> | |
| 57 <filter type="sort_by" column="2"/> | |
| 58 <validator type="no_options" message="No indexes are available for the selected input dataset"/> | |
| 59 </options> | |
| 60 </param> | |
| 61 </inputs> | |
| 62 <outputs> | |
| 63 <data format="sam" name="outalign" label="outalign.sam" /> | |
| 64 <data format="fastqsanger" name="pathomap_appendAlign" label="pathomap_appendAlign.fastq" /> | |
| 65 </outputs> | |
| 66 | |
| 67 <help> | |
| 68 IMPORTANT: The name and the path of the reference database (with bowtie indexed) | |
| 69 should be added to the pathoscope.loc entry. | |
| 70 </help> | |
| 71 <citations> | |
| 72 <citation type="doi">10.1101/gr.150151.112</citation> | |
| 73 <citation type="doi">10.1186/2049-2618-2-33</citation> | |
| 74 <citation type="doi">10.1186/1471-2105-15-262</citation> | |
| 75 <citation type="doi">10.4137/CIN.S13890</citation> | |
| 76 </citations> | |
| 77 </tool> |