Mercurial > repos > drosofff > msp_sr_bowtie_parser
comparison sRbowtieParser.xml @ 1:ca3845fb0b31 draft default tip
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie_parser commit 70312b58ba246c07e70cdbd0a097f274f1386d09
| author | drosofff |
|---|---|
| date | Mon, 18 Apr 2016 10:09:08 -0400 |
| parents | b996480cd604 |
| children |
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| 0:b996480cd604 | 1:ca3845fb0b31 |
|---|---|
| 1 <tool id="sRbowtieParser" name="Parse items in sRbowtie alignment" version="1.0.1"> | 1 <tool id="sRbowtieParser" name="Parse items in sRbowtie alignment" version="1.0.6"> |
| 2 <description></description> | 2 <description></description> |
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="package" version="0.12.7">bowtie</requirement> | 4 <requirement type="package" version="0.12.7">bowtie</requirement> |
| 5 <requirement type="package" version="0.1.18">samtools</requirement> | |
| 6 <requirement type="package" version="0.7.7">pysam</requirement> | 5 <requirement type="package" version="0.7.7">pysam</requirement> |
| 7 <requirement type="package" version="1.9">numpy</requirement> | 6 <requirement type="package" version="1.9">numpy</requirement> |
| 8 <requirement type="package" version="0.14">scipy</requirement> | |
| 9 </requirements> | 7 </requirements> |
| 10 <command interpreter="python"> | 8 <command> |
| 11 sRbowtieParser.py | 9 python $__tool_directory__/sRbowtieParser.py |
| 12 #if $refGenomeSource.genomeSource == "history": | 10 #if $refGenomeSource.genomeSource == "history": |
| 13 --IndexSource $refGenomeSource.ownFile | 11 --IndexSource $refGenomeSource.ownFile |
| 14 --ExtractDirective fastaSource | 12 --ExtractDirective fastaSource |
| 15 #else: | 13 #else: |
| 16 #silent reference= filter( lambda x: str( x[0] ) == str( $input_list.dbkey ), $__app__.tool_data_tables[ 'bowtie_indexes' ].get_fields() )[0][-1] | 14 #silent reference= filter( lambda x: str( x[0] ) == str( $input_list.dbkey ), $__app__.tool_data_tables[ 'bowtie_indexes' ].get_fields() )[0][-1] |
| 27 #for $i in $refGenomeSource.input_list | 25 #for $i in $refGenomeSource.input_list |
| 28 $i.ext | 26 $i.ext |
| 29 #end for | 27 #end for |
| 30 --alignmentLabel | 28 --alignmentLabel |
| 31 #for $i in $refGenomeSource.input_list | 29 #for $i in $refGenomeSource.input_list |
| 32 "$i.name" | 30 "$i.element_identifier" |
| 33 #end for | 31 #end for |
| 34 | 32 |
| 35 </command> | 33 </command> |
| 36 <inputs> | 34 <inputs> |
| 37 <conditional name="refGenomeSource"> | 35 <conditional name="refGenomeSource"> |
| 38 <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options"> | 36 <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options"> |
| 39 <option value="indexed">Use a built-in index</option> | 37 <option value="indexed">Use a built-in index</option> |
| 40 <option value="history">Use one from the history</option> | 38 <option value="history">Use one from the history</option> |
| 41 </param> | 39 </param> |
| 42 <when value="indexed"> | 40 <when value="indexed"> |
| 43 <param name="input_list" type="data" label="Select multiple alignments to parse" multiple="true"> | 41 <param name="input_list" type="data" format="tabular,sam,bam" label="Select multiple alignments to parse" multiple="true"> |
| 44 <validator type="dataset_metadata_in_data_table" table_name="bowtie_indexes" metadata_name="dbkey" metadata_column="0" message="database not set for this bowtie output. Select the database(=genome used for matching) manually, or select a reference fasta from your history."/> | 42 <validator type="dataset_metadata_in_data_table" table_name="bowtie_indexes" metadata_name="dbkey" metadata_column="0" message="database not set for this bowtie output. Select the database(=genome used for matching) manually, or select a reference fasta from your history."/> |
| 45 </param> | 43 </param> |
| 46 </when> | 44 </when> |
| 47 <when value="history"> | 45 <when value="history"> |
| 48 <param name="ownFile" type="data" format="fasta" label="Select the fasta reference" /> | 46 <param name="ownFile" type="data" format="fasta" label="Select the fasta reference" /> |
| 49 <param name="input_list" type="data" label="Select multiple alignments to parse" multiple="true"/> | 47 <param name="input_list" type="data" format="tabular,sam,bam" label="Select multiple alignments to parse" multiple="true"/> |
| 50 </when> | 48 </when> |
| 51 </conditional> <!-- refGenomeSource --> | 49 </conditional> <!-- refGenomeSource --> |
| 52 <param name="polarity" type="select" label="how to count sense and antisense reads"> | 50 <param name="polarity" type="select" label="how to count sense and antisense reads"> |
| 53 <option value="both">count both sense and antisense reads</option> | 51 <option value="both">count both sense and antisense reads</option> |
| 54 <option value="forward">count only sense reads</option> | 52 <option value="forward">count only sense reads</option> |