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comparison bwa_macros.xml @ 2:b4dfb5470bf3 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 13b3ab10ff1a2e4be39b44f885df6bbe7c23099a
author devteam
date Fri, 30 Dec 2016 08:10:56 -0500
parents 8955a9521def
children b59a6178a6e0
comparison
equal deleted inserted replaced
1:8955a9521def 2:b4dfb5470bf3
1 <macros> 1 <macros>
2 <import>read_group_macros.xml</import> 2 <import>read_group_macros.xml</import>
3
4 <token name="@VERSION@">0.7.15</token>
5
3 <token name="@set_rg_string@"> 6 <token name="@set_rg_string@">
4 #set $rg_string = "@RG\\tID:" + str($rg_id) 7 #set $rg_string = "@RG\\tID:" + str($rg_id)
5 #set $rg_string += $format_read_group("\\tSM:", $rg_sm) 8 #set $rg_string += $format_read_group("\\tSM:", $rg_sm)
6 #set $rg_string += $format_read_group("\\tPL:", $rg_pl) 9 #set $rg_string += $format_read_group("\\tPL:", $rg_pl)
7 #set $rg_string += $format_read_group("\\tLB:", $rg_lb) 10 #set $rg_string += $format_read_group("\\tLB:", $rg_lb)
13 #set $rg_string += $format_read_group("\\tPG:", $rg_pg) 16 #set $rg_string += $format_read_group("\\tPG:", $rg_pg)
14 #set $rg_string += $format_read_group("\\tPI:", $rg_pi) 17 #set $rg_string += $format_read_group("\\tPI:", $rg_pi)
15 #set $rg_string += $format_read_group("\\tPU:", $rg_pu) 18 #set $rg_string += $format_read_group("\\tPU:", $rg_pu)
16 </token> 19 </token>
17 20
21 <token name="@set_reference_fasta_filename@"><![CDATA[
22 #if str( $reference_source.reference_source_selector ) == "history":
23 #set $reference_fasta_filename = "localref.fa"
24 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &&
25 bwa index
26 #if str($reference_source.index_a) != 'auto'
27 -a ${reference_source.index_a}
28 #end if
29 "${reference_fasta_filename}" &&
30 #else:
31 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
32 #end if
33 ]]></token>
34
18 <xml name="requirements"> 35 <xml name="requirements">
19 <requirements> 36 <requirements>
20 <requirement type="package" version="0.7.12">bwa</requirement> 37 <requirement type="package" version="@VERSION@">bwa</requirement>
21 <requirement type="package" version="1.2">samtools</requirement> 38 <requirement type="package" version="1.3.1">samtools</requirement>
22 </requirements> 39 </requirements>
23 </xml> 40 </xml>
24 41
25 <xml name="stdio"> 42 <xml name="stdio">
26 <stdio> 43 <stdio>
28 <exit_code range=":-1" /> 45 <exit_code range=":-1" />
29 <regex match="Error:" /> 46 <regex match="Error:" />
30 <regex match="Exception:" /> 47 <regex match="Exception:" />
31 </stdio> 48 </stdio>
32 </xml> 49 </xml>
50
51 <macro name="reference_source_conditional">
52 <conditional name="reference_source">
53 <param name="reference_source_selector" 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. See `Indexes` section of help below">
54 <option value="cached">Use a built-in genome index</option>
55 <option value="history">Use a genome from history and build index</option>
56 </param>
57 <when value="cached">
58 <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list">
59 <options from_data_table="bwa_mem_indexes">
60 <filter type="sort_by" column="2" />
61 <validator type="no_options" message="No indexes are available" />
62 </options>
63 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
64 </param>
65 </when>
66 <when value="history">
67 <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence" help="You can upload a FASTA sequence to the history and use it as reference" />
68 <param name="index_a" type="select" label="Algorithm for constructing the BWT index" help="(-a)">
69 <option value="auto">Auto. Let BWA decide the best algorithm to use</option>
70 <option value="is">IS linear-time algorithm for constructing suffix array. It requires 5.37N memory where N is the size of the database. IS is moderately fast, but does not work with database larger than 2GB</option>
71 <option value="bwtsw">BWT-SW algorithm. This method works also with big genomes</option>
72 </param>
73 </when>
74 </conditional>
75 </macro>
33 76
34 <macro name="dbKeyActionsBwa"> 77 <macro name="dbKeyActionsBwa">
35 <expand macro="dbKeyActions"> 78 <expand macro="dbKeyActions">
36 <option type="from_data_table" name="bwa_indexes" column="1" offset="0"> 79 <option type="from_data_table" name="bwa_indexes" column="1" offset="0">
37 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> 80 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
129 172
130 1. https://biostar.usegalaxy.org/ 173 1. https://biostar.usegalaxy.org/
131 2. https://www.biostars.org/ 174 2. https://www.biostars.org/
132 3. https://github.com/lh3/bwa 175 3. https://github.com/lh3/bwa
133 4. http://bio-bwa.sourceforge.net/ 176 4. http://bio-bwa.sourceforge.net/
134 177
135 </token> 178 </token>
136 179
137 <token name="@dataset_collections@"> 180 <token name="@dataset_collections@">
138 ------ 181 ------
139 182
140 **Dataset collections - processing large numbers of datasets at once** 183 **Dataset collections - processing large numbers of datasets at once**
141 184