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comparison bowtie2_wrapper.xml @ 5:42bb952b4e3c draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
author devteam
date Tue, 21 Jul 2015 13:01:59 -0400
parents 1fc845afa3ac
children e23b0cdeeba6
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4:1fc845afa3ac 5:42bb952b4e3c
1 <tool id="bowtie2" name="Bowtie2" version="0.5"> 1 <tool id="bowtie2" name="Bowtie2" version="0.6">
2 <!-- Wrapper compatible with Bowtie version 2.2.4 --> 2 <!-- Wrapper compatible with Bowtie version 2.2.4 -->
3 <description>- map reads against reference genome</description> 3 <description>- map reads against reference genome</description>
4 <macros>
5 <import>read_group_macros.xml</import>
6 </macros>
4 <version_command>bowtie2 --version</version_command> 7 <version_command>bowtie2 --version</version_command>
5 <requirements> 8 <requirements>
6 <requirement type="package" version="2.2.4">bowtie2</requirement> 9 <requirement type="package" version="2.2.4">bowtie2</requirement>
7 <requirement type="package" version="0.1.18">samtools</requirement> 10 <requirement type="package" version="0.1.18">samtools</requirement>
8 </requirements> 11 </requirements>
68 #if str( $library.unaligned_file ) == "true": 71 #if str( $library.unaligned_file ) == "true":
69 --un-conc $output_unaligned_reads_l 72 --un-conc $output_unaligned_reads_l
70 #end if 73 #end if
71 #end if 74 #end if
72 75
73 ## Readgroups 76 ## Read group information.
74 #if str( $read_group.read_group_selector ) == "yes": 77 @define_read_group_helpers@
75 --rg-id "${read_group.rgid}" 78 #if str( $library.type ) == "single":
76 --rg "SM:${read_group.rgsm}" 79 #set $rg_auto_name = $read_group_name_default($library.input_1)
77 --rg "LB:${read_group.rglb}" 80 #elif str( $library.type ) == "paired":
78 --rg "PL:${read_group.rgpl}" 81 #set $rg_auto_name = $read_group_name_default($library.input_1, $library.input_2)
82 #else
83 #set $rg_auto_name = $read_group_name_default($library.input_1)
84 #end if
85 @set_use_rg_var@
86 @set_read_group_vars@
87 #if $use_rg
88 $format_read_group("", $rg_id, '"', arg='--rg-id ')
89 $format_read_group("SM:", $rg_sm, '"', arg='--rg ')
90 $format_read_group("PL:", $rg_pl, '"', arg='--rg ')
91 $format_read_group("LB:", $rg_lb, '"', arg='--rg ')
92 $format_read_group("CN:", $rg_cn, '"', arg='--rg ')
93 $format_read_group("DS:", $rg_ds, '"', arg='--rg ')
94 $format_read_group("DT:", $rg_dt, '"', arg='--rg ')
95 $format_read_group("FO:", $rg_fo, '"', arg='--rg ')
96 $format_read_group("KS:", $rg_ks, '"', arg='--rg ')
97 $format_read_group("PG:", $rg_pg, '"', arg='--rg ')
98 $format_read_group("PI:", $rg_pi, '"', arg='--rg ')
99 $format_read_group("PU:", $rg_pu, '"', arg='--rg ')
79 #end if 100 #end if
80 101
81 ## Analysis type 102 ## Analysis type
82 #if ( str( $analysis_type.analysis_type_selector ) == "simple" and str( $analysis_type.presets ) != "no_presets" ): 103 #if ( str( $analysis_type.analysis_type_selector ) == "simple" and str( $analysis_type.presets ) != "no_presets" ):
83 $analysis_type.presets 104 $analysis_type.presets
255 <param name="own_file" type="data" format="fasta" metadata_name="dbkey" label="Select reference genome" /> 276 <param name="own_file" type="data" format="fasta" metadata_name="dbkey" label="Select reference genome" />
256 </when> 277 </when>
257 </conditional> 278 </conditional>
258 279
259 <!-- read group settings --> 280 <!-- read group settings -->
260 <conditional name="read_group"> 281 <expand macro="read_group_conditional" />
261 <param name="read_group_selector" type="select" label="Specify the read group for this file?" help="Specifying readgroup information can greatly simplify your downstream analyses by allowing combining multiple datasets. See help below for more details">
262 <option value="yes">Yes</option>
263 <option value="no" selected="True">No</option>
264 </param>
265 <when value="yes">
266 <param name="rgid" type="text" size="25" label="Read group identifier (ID). Each @RG line must have a unique ID. The value of ID is used in the RG tags of alignment records. Must be unique among all read groups in header section." help="--rg-id; Required if RG specified. Read group IDs may be modified when merging SAM files in order to handle collisions." />
267 <param name="rglb" type="text" size="25" label="Library name (LB)" help="--rg; Required if RG specified" />
268 <param name="rgpl" type="text" size="25" label="Platform/technology used to produce the reads (PL)" help="--rg; Required if RG specified. Valid values : CAPILLARY, LS454, ILLUMINA, SOLID, HELICOS, IONTORRENT and PACBIO" />
269 <param name="rgsm" type="text" size="25" label="Sample (SM)" help="--rg; Required if RG specified. Use pool name where a pool is being sequenced" />
270 </when>
271 <when value="no" />
272 </conditional>
273
274 <conditional name="analysis_type"> 282 <conditional name="analysis_type">
275 <param name="analysis_type_selector" type="select" label="Select analysis mode"> 283 <param name="analysis_type_selector" type="select" label="Select analysis mode">
276 <option value="simple">1: Default setting only</option> 284 <option value="simple">1: Default setting only</option>
277 <option value="full">2: Full parameter list</option> 285 <option value="full">2: Full parameter list</option>
278 </param> 286 </param>
477 <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/> 485 <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/>
478 <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/> 486 <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/>
479 <param name="own_file" value="bowtie2-ref.fasta" /> 487 <param name="own_file" value="bowtie2-ref.fasta" />
480 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/> 488 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>
481 </test> 489 </test>
490 <test>
491 <!-- basic test on single paired default run -->
492 <param name="type" value="paired"/>
493 <param name="selection" value="no"/>
494 <param name="paired_options_selector" value="no"/>
495 <param name="unaligned_file" value="false"/>
496 <param name="analysis_type_selector" value="simple"/>
497 <param name="rg_selector" value="set"/>
498 <param name="ID" value="rg1"/>
499 <param name="PL" value="CAPILLARY"/>
500 <param name="source" value="history" />
501 <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/>
502 <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/>
503 <param name="own_file" value="bowtie2-ref.fasta" />
504 <output name="output" file="bowtie2-test2.bam" ftype="bam" lines_diff="2"/>
505 </test>
482 </tests> 506 </tests>
483 507
484 <help> 508 <help>
485 509
486 **Bowtie2 Overview** 510 **Bowtie2 Overview**