Mercurial > repos > devteam > bwa
diff bwa_macros.xml @ 18:48f306c57611 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
| author | iuc |
|---|---|
| date | Fri, 24 Nov 2017 09:55:45 -0500 |
| parents | be4e38d127ae |
| children | dfd8b7f78c37 |
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--- a/bwa_macros.xml Tue Nov 21 11:24:01 2017 -0500 +++ b/bwa_macros.xml Fri Nov 24 09:55:45 2017 -0500 @@ -1,115 +1,115 @@ <macros> - <import>read_group_macros.xml</import> + <import>read_group_macros.xml</import> - <token name="@VERSION@">0.7.17</token> + <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_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[ + <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> - </requirements> - </xml> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@VERSION@">bwa</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> + <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="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="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="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> + <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@"> + <token name="@RG@"> ----- .. class:: warningmark @@ -160,8 +160,8 @@ @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@"> + </token> + <token name="@info@"> ----- .. class:: infomark @@ -175,16 +175,5 @@ 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> - + </token> </macros>