Mercurial > repos > devteam > bowtie2
comparison bowtie2_wrapper.xml @ 5:42bb952b4e3c draft
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** |