| Previous changeset 4:1fc845afa3ac (2015-07-21) Next changeset 6:e23b0cdeeba6 (2015-08-26) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty |
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modified:
bowtie2_wrapper.xml |
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added:
read_group_macros.xml test-data/bowtie2-test2.bam |
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| diff -r 1fc845afa3ac -r 42bb952b4e3c bowtie2_wrapper.xml --- a/bowtie2_wrapper.xml Tue Jul 21 13:00:51 2015 -0400 +++ b/bowtie2_wrapper.xml Tue Jul 21 13:01:59 2015 -0400 |
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| @@ -1,6 +1,9 @@ -<tool id="bowtie2" name="Bowtie2" version="0.5"> +<tool id="bowtie2" name="Bowtie2" version="0.6"> <!-- Wrapper compatible with Bowtie version 2.2.4 --> <description>- map reads against reference genome</description> + <macros> + <import>read_group_macros.xml</import> + </macros> <version_command>bowtie2 --version</version_command> <requirements> <requirement type="package" version="2.2.4">bowtie2</requirement> @@ -70,12 +73,30 @@ #end if #end if - ## Readgroups - #if str( $read_group.read_group_selector ) == "yes": - --rg-id "${read_group.rgid}" - --rg "SM:${read_group.rgsm}" - --rg "LB:${read_group.rglb}" - --rg "PL:${read_group.rgpl}" + ## Read group information. + @define_read_group_helpers@ + #if str( $library.type ) == "single": + #set $rg_auto_name = $read_group_name_default($library.input_1) + #elif str( $library.type ) == "paired": + #set $rg_auto_name = $read_group_name_default($library.input_1, $library.input_2) + #else + #set $rg_auto_name = $read_group_name_default($library.input_1) + #end if + @set_use_rg_var@ + @set_read_group_vars@ + #if $use_rg + $format_read_group("", $rg_id, '"', arg='--rg-id ') + $format_read_group("SM:", $rg_sm, '"', arg='--rg ') + $format_read_group("PL:", $rg_pl, '"', arg='--rg ') + $format_read_group("LB:", $rg_lb, '"', arg='--rg ') + $format_read_group("CN:", $rg_cn, '"', arg='--rg ') + $format_read_group("DS:", $rg_ds, '"', arg='--rg ') + $format_read_group("DT:", $rg_dt, '"', arg='--rg ') + $format_read_group("FO:", $rg_fo, '"', arg='--rg ') + $format_read_group("KS:", $rg_ks, '"', arg='--rg ') + $format_read_group("PG:", $rg_pg, '"', arg='--rg ') + $format_read_group("PI:", $rg_pi, '"', arg='--rg ') + $format_read_group("PU:", $rg_pu, '"', arg='--rg ') #end if ## Analysis type @@ -257,20 +278,7 @@ </conditional> <!-- read group settings --> - <conditional name="read_group"> - <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"> - <option value="yes">Yes</option> - <option value="no" selected="True">No</option> - </param> - <when value="yes"> - <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." /> - <param name="rglb" type="text" size="25" label="Library name (LB)" help="--rg; Required if RG specified" /> - <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" /> - <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" /> - </when> - <when value="no" /> - </conditional> - + <expand macro="read_group_conditional" /> <conditional name="analysis_type"> <param name="analysis_type_selector" type="select" label="Select analysis mode"> <option value="simple">1: Default setting only</option> @@ -479,6 +487,22 @@ <param name="own_file" value="bowtie2-ref.fasta" /> <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/> </test> + <test> + <!-- basic test on single paired default run --> + <param name="type" value="paired"/> + <param name="selection" value="no"/> + <param name="paired_options_selector" value="no"/> + <param name="unaligned_file" value="false"/> + <param name="analysis_type_selector" value="simple"/> + <param name="rg_selector" value="set"/> + <param name="ID" value="rg1"/> + <param name="PL" value="CAPILLARY"/> + <param name="source" value="history" /> + <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/> + <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/> + <param name="own_file" value="bowtie2-ref.fasta" /> + <output name="output" file="bowtie2-test2.bam" ftype="bam" lines_diff="2"/> + </test> </tests> <help> |
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| diff -r 1fc845afa3ac -r 42bb952b4e3c read_group_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/read_group_macros.xml Tue Jul 21 13:01:59 2015 -0400 |
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| b'@@ -0,0 +1,294 @@\n+<macros>\n+ <!-- Import this at the top of your command block and then\n+ define rg_auto_name. -->\n+ <token name="@define_read_group_helpers@">\n+#import re\n+#def identifier_or_name($input1)\n+ #if hasattr($input1, \'element_identifier\')\n+ #return $input1.element_identifier\n+ #else\n+ #return $input1.name.rstrip(\'.gz\').rstrip(\'.fastq\').rstrip(\'.fq\')\n+ #end if\n+#end def\n+\n+#def clean(name)\n+ #set $name_clean = re.sub(\'[^\\w\\-_\\.]\', \'_\', $name)\n+ #return $name_clean\n+#end def\n+\n+#def read_group_name_default($input1, $input2=None)\n+ #if $input2 is None\n+ #return $clean($identifier_or_name($input1))\n+ #else\n+ #import itertools\n+ #set $input_name1 = $clean($identifier_or_name($input1))\n+ #set $input_name2 = $clean($identifier_or_name($input2))\n+ #set $common_prefix = \'\'.join([c[0] for c in itertools.takewhile(lambda x: all(x[0] == y for y in x), itertools.izip(*[$input_name1, $input_name2]))])\n+ #if len($common_prefix) > 3\n+ #return $common_prefix\n+ #else\n+ #return $input_name1\n+ #end if\n+ #end if\n+#end def\n+\n+#def format_read_group(prefix, value, quote=\'\', arg=\'\')\n+ #if $value\n+ #return $arg + $quote + $prefix + $value + $quote\n+ #else\n+ #return \'\'\n+ #end if\n+#end def\n+\n+#def rg_param(name)\n+ #if $varExists("rg")\n+ #return $rg.get($name, None)\n+ #else\n+ #return $getVar($name, None)\n+ #end if\n+#end def\n+\n+#set $use_rg = True\n+ </token>\n+ <!-- preconditions use_rg and rg_auto_name have been\n+ defined.\n+ -->\n+ <token name="@set_read_group_vars@">\n+#if $use_rg\n+ #if $rg_param(\'read_group_id_conditional\') is None\n+ #set $rg_id = $rg_auto_name\n+ #elif $rg_param(\'read_group_id_conditional\').do_auto_name\n+ #set $rg_id = $rg_auto_name\n+ #else\n+ #set $rg_id = str($rg_param(\'read_group_id_conditional\').ID)\n+ #end if\n+\n+ #if $rg_param(\'read_group_sm_conditional\') is None\n+ #set $rg_sm = \'\'\n+ #elif $rg_param(\'read_group_sm_conditional\').do_auto_name\n+ #set $rg_sm = $rg_auto_name\n+ #else\n+ #set $rg_sm = str($rg_param(\'read_group_sm_conditional\').SM)\n+ #end if\n+\n+ #if $rg_param(\'PL\')\n+ #set $rg_pl = str($rg_param(\'PL\'))\n+ #else\n+ #set $rg_pl = \'\'\n+ #end if\n+\n+ #if $rg_param(\'read_group_lb_conditional\') is None\n+ #set $rg_lb = \'\'\n+ #elif $rg_param(\'read_group_lb_conditional\')do_auto_name\n+ #set $rg_lb = $rg_auto_name\n+ #else\n+ #set $rg_lb = str($rg_param(\'read_group_lb_conditional\').LB)\n+ #end if\n+\n+ #if $rg_param(\'CN\')\n+ #set $rg_cn = str($rg_param(\'CN\'))\n+ #else\n+ #set $rg_cn = \'\'\n+ #end if\n+\n+ #if $rg_param("DS")\n+ #set $rg_ds = str($rg_param("DS"))\n+ #else\n+ #set $rg_ds = \'\'\n+ #end if\n+\n+ #if $rg_param("DT")\n+ #set $rg_dt = str($rg_param("DT"))\n+ #else\n+ #set $rg_dt = \'\'\n+ #end if\n+\n+ #if $rg_param("FO")\n+ #set $rg_fo = str($rg_param("FO"))\n+ #else\n+ #set $rg_fo = \'\'\n+ #end if\n+\n+ #if $rg_param("KS")\n+ #set $rg_ks = str($rg_param("KS"))\n+ #else\n+ #set $rg_ks = \'\'\n+ #end if\n+\n+ #if $rg_param("PG")\n+ #set $rg_pg = str($rg_param("PG"))\n+ #else\n+ #set $rg_pg = \'\'\n+ #end if\n+\n+ #if str($rg_param("PI"))\n+ #set $rg_pi = str($rg_param("PI"))\n+ #else\n+ #set $rg_pi = \'\'\n+ #end if\n+\n+ #if $rg_param("PU")\n+ #set $rg_pu = str($rg_param("PU"))\n+ #else\n+ #set $rg_pu = \'\'\n+ #end if\n+#end if\n+ </token>\n+ <token name="@set_use_rg_var@">\n+#set $use_rg = str($rg.rg_selector) != "do_not_set"\n+ </token>\n+ <xml name="read_group_auto_name_conditional">\n+ <param name="do_auto_name" type="boolean" label="Auto-assign" help="Use dataset name or collection information to automatically assign this value" checked="no" />\n+ <when value="true">'..b'd_group_dt_param">\n+ <param name="DT" type="text" size="25" label="Date that run was produced (DT)" help="ISO8601 format date or date/time, like YYYY-MM-DD" />\n+ </xml>\n+ <xml name="read_group_fo_param">\n+ <param name="FO" type="text" size="25" optional="true" label="Flow order (FO)" help="The array of nucleotide bases that correspond to the nucleotides used for each flow of each read. Multi-base flows are encoded in IUPAC format, and non-nucleotide flows by various other characters. Format: /\\*|[ACMGRSVTWYHKDBN]+/">\n+ <validator type="regex" message="Invalid flow order">\\*|[ACMGRSVTWYHKDBN]+$</validator>\n+ </param>\n+ </xml>\n+ <xml name="read_group_ks_param">\n+ <param name="KS" type="text" size="25" label="The array of nucleotide bases that correspond to the key sequence of each read (KS)" />\n+ </xml>\n+ <xml name="read_group_pg_param">\n+ <param name="PG" type="text" size="25" label="Programs used for processing the read group (PG)" />\n+ </xml>\n+ <xml name="read_group_pi_param">\n+ <param name="PI" type="integer" optional="true" label="Predicted median insert size (PI)" />\n+ </xml>\n+ <xml name="read_group_pu_param">\n+ <param name="PU" type="text" size="25" label="Platform unit (PU)" help="Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)" optional="True" />\n+ </xml>\n+ <xml name="read_group_pu_required_param">\n+ <param name="PU" type="text" size="25" label="Platform unit (PU)" help="Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)" optional="False" />\n+ </xml>\n+ <!-- Only ID is required - all groups available -->\n+ <xml name="read_group_inputs_spec">\n+ <expand macro="read_group_id_conditional" />\n+ <expand macro="read_group_sm_conditional" />\n+ <expand macro="read_group_pl_param" />\n+ <expand macro="read_group_lb_conditional" />\n+ <expand macro="read_group_cn_param" />\n+ <expand macro="read_group_ds_param" />\n+ <expand macro="read_group_dt_param" />\n+ <expand macro="read_group_fo_param" />\n+ <expand macro="read_group_ks_param" />\n+ <expand macro="read_group_pg_param" />\n+ <expand macro="read_group_pi_param" />\n+ <expand macro="read_group_pu_param" />\n+ </xml>\n+ <!-- ID, SM, LB, PU, PL all required - not ks, pg, or fo params. -->\n+ <xml name="read_group_inputs_picard">\n+ <expand macro="read_group_id_conditional" />\n+ <expand macro="read_group_sm_required_conditional" />\n+ <expand macro="read_group_lb_required_conditional" />\n+ <expand macro="read_group_pl_param" />\n+ <expand macro="read_group_pu_required_param" />\n+ <expand macro="read_group_cn_param" />\n+ <expand macro="read_group_ds_param" />\n+ <expand macro="read_group_pi_param" />\n+ <expand macro="read_group_dt_param" />\n+ </xml>\n+ <xml name="read_group_conditional">\n+ <conditional name="rg">\n+ <param name="rg_selector" type="select" label="Set read groups information?" help="Specifying read group information can greatly simplify your downstream analyses by allowing combining multiple datasets.">\n+ <option value="set">Set read groups (SAM/BAM specification)</option>\n+ <option value="set_picard">Set read groups (Picard style)</option>\n+ <option value="set_id_auto">Automatically assign ID</option>\n+ <option value="do_not_set" selected="True">Do not set</option>\n+ </param>\n+ <when value="set_picard">\n+ <expand macro="read_group_inputs_picard" />\n+ </when>\n+ <when value="set">\n+ <expand macro="read_group_inputs_spec" />\n+ </when>\n+ <when value="set_id_auto">\n+ </when>\n+ <when value="do_not_set">\n+ </when>\n+ </conditional>\n+ </xml>\n+</macros>\n' |
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| diff -r 1fc845afa3ac -r 42bb952b4e3c test-data/bowtie2-test2.bam |
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| Binary file test-data/bowtie2-test2.bam has changed |