bwa: bwa_macros.xml comparison

comparison bwa_macros.xml @ 8:cbc665adcde4 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396

author	iuc
date	Fri, 24 Nov 2017 09:55:28 -0500
parents	a4d167793afa
children	a628f5606f68

comparison

equal deleted inserted replaced

-:c022e4a68b76
+:cbc665adcde4
 <macros>
 <import>read_group_macros.xml</import>
 <token name="@VERSION@">0.7.17</token>
 <token name="@set_rg_string@">
 #set $rg_string = "@RG\\tID:" + str($rg_id)
 #set $rg_string += $format_read_group("\\tSM:", $rg_sm)
 #set $rg_string += $format_read_group("\\tPL:", $rg_pl)
 #set $rg_string += $format_read_group("\\tLB:", $rg_lb)
 #set $rg_string += $format_read_group("\\tCN:", $rg_cn)
 #set $rg_string += $format_read_group("\\tDS:", $rg_ds)
 #set $rg_string += $format_read_group("\\tDT:", $rg_dt)
 #set $rg_string += $format_read_group("\\tFO:", $rg_fo)
 #set $rg_string += $format_read_group("\\tKS:", $rg_ks)
 #set $rg_string += $format_read_group("\\tPG:", $rg_pg)
 #set $rg_string += $format_read_group("\\tPI:", $rg_pi)
 #set $rg_string += $format_read_group("\\tPU:", $rg_pu)
 </token>
 <token name="@set_reference_fasta_filename@"><![CDATA[
 #if str( $reference_source.reference_source_selector ) == "history":
 #set $reference_fasta_filename = "localref.fa"
-ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &&
+ln -s '${reference_source.ref_file}' '${reference_fasta_filename}' &&
 bwa index
 #if str($reference_source.index_a) != 'auto'
 -a ${reference_source.index_a}
 #end if
-"${reference_fasta_filename}" &&
+'${reference_fasta_filename}' &&
 #else:
 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
 #end if
 ]]></token>
 <xml name="requirements">
 <requirements>
 <requirement type="package" version="@VERSION@">bwa</requirement>
-<requirement type="package" version="1.5">samtools</requirement>
+<requirement type="package" version="1.6">samtools</requirement>
 </requirements>
 </xml>
 <xml name="stdio">
 <stdio>
 <exit_code range="1:" />
 <exit_code range=":-1" />
 <regex match="Error:" />
 <regex match="Exception:" />
 </stdio>
 </xml>
 <macro name="reference_source_conditional">
 <conditional name="reference_source">
 <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">
 <option value="cached">Use a built-in genome index</option>
 <option value="history">Use a genome from history and build index</option>
 </param>
 <when value="cached">
 <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list">
 <options from_data_table="bwa_mem_indexes">
 <filter type="sort_by" column="2" />
 <validator type="no_options" message="No indexes are available" />
 </options>
 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
 </param>
 </when>
 <when value="history">
 <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" />
 <param name="index_a" type="select" label="Algorithm for constructing the BWT index" help="(-a)">
 <option value="auto">Auto. Let BWA decide the best algorithm to use</option>
 <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>
 <option value="bwtsw">BWT-SW algorithm. This method works also with big genomes</option>
 </param>
 </when>
 </conditional>
 </macro>
 <macro name="dbKeyActionsBwa">
 <expand macro="dbKeyActions">
 <option type="from_data_table" name="bwa_indexes" column="1" offset="0">
 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
 <filter type="param_value" ref="reference_source.ref_file" column="0"/>
 </option>
 </expand>
 </macro>
 <macro name="dbKeyActionsBwaMem">
 <expand macro="dbKeyActions">
 <option type="from_data_table" name="bwa_mem_indexes" column="1" offset="0">
 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
 <filter type="param_value" ref="reference_source.ref_file" column="0"/>
 </option>
 </expand>
 </macro>
 <macro name="dbKeyActions">
 <actions>
 <conditional name="reference_source.reference_source_selector">
 <when value="cached">
 <action type="metadata" name="dbkey">
 <yield />
 </action>
 </when>
 <when value="history">
 <action type="metadata" name="dbkey">
 <option type="from_param" name="reference_source.ref_file" param_attribute="dbkey" />
 </action>
 </when>
 </conditional>
 </actions>
 </macro>
 <token name="@RG@">
 -----
 .. class:: warningmark
 **Read Groups are Important!**
 @RG     ID:FLOWCELL2.LANE2      PL:illumina     LB:LIB-KID-1 SM:KID      PI:200
 @RG     ID:FLOWCELL2.LANE3      PL:illumina     LB:LIB-KID-2 SM:KID      PI:400
 @RG     ID:FLOWCELL2.LANE4      PL:illumina     LB:LIB-KID-2 SM:KID      PI:400
 Note the hierarchical relationship between read groups (unique for each lane) to libraries (sequenced on two lanes) and samples (across four lanes, two lanes for each library).
 </token>
 <token name="@info@">
 -----
 .. class:: infomark
 **More info**
 1. https://biostar.usegalaxy.org/
 2. https://www.biostars.org/
 3. https://github.com/lh3/bwa
 4. http://bio-bwa.sourceforge.net/
 </token>
-<token name="@dataset_collections@">
-------
-**Dataset collections - processing large numbers of datasets at once**
-Dataset collections are in beta-testing. Extensive documentation will be added later this Spring.
-</token>
 </macros>

Mercurial > repos > devteam > bwa

comparison bwa_macros.xml @ 8:cbc665adcde4 draft