| Previous changeset 6:e23b0cdeeba6 (2015-08-26) Next changeset 8:82414e16b6bd (2015-11-16) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7 |
|
modified:
bowtie2_wrapper.xml read_group_macros.xml |
| b |
| diff -r e23b0cdeeba6 -r 4f92dccc808a bowtie2_wrapper.xml --- a/bowtie2_wrapper.xml Wed Aug 26 12:46:11 2015 -0400 +++ b/bowtie2_wrapper.xml Wed Nov 11 12:04:23 2015 -0500 |
| [ |
| b'@@ -10,7 +10,7 @@\n <requirement type="package" version="0.1.18">samtools</requirement>\n </requirements>\n <command>\n- \n+\n ## prepare bowtie2 index\n #set index_path = \'\'\n #if str($reference_genome.source) == "history":\n@@ -20,18 +20,17 @@\n #else:\n #set index_path = $reference_genome.index.fields.path\n #end if\n- \n+\n ## execute bowtie2\n- \n+\n bowtie2\n- \n+\n ## number of threads\n -p \\${GALAXY_SLOTS:-4}\n \n ## index file path\n -x $index_path\n- \n- \n+\n ## Fastq inputs\n #if str( $library.type ) == "single":\n -U "${library.input_1}"\n@@ -72,7 +71,7 @@\n --un-conc $output_unaligned_reads_l\n #end if\n #end if\n- \n+\n ## Read group information.\n @define_read_group_helpers@\n #if str( $library.type ) == "single":\n@@ -98,7 +97,7 @@\n $format_read_group("PI:", $rg_pi, \'"\', arg=\'--rg \')\n $format_read_group("PU:", $rg_pu, \'"\', arg=\'--rg \')\n #end if\n- \n+\n ## Analysis type\n #if ( str( $analysis_type.analysis_type_selector ) == "simple" and str( $analysis_type.presets ) != "no_presets" ):\n $analysis_type.presets\n@@ -112,7 +111,7 @@\n ${analysis_type.input_options.solexa_quals}\n ${analysis_type.input_options.int_quals}\n #end if\n- \n+\n #if str( $analysis_type.alignment_options.alignment_options_selector ) == "yes":\n -N "${analysis_type.alignment_options.N}"\n -L "${analysis_type.alignment_options.L}"\n@@ -132,7 +131,7 @@\n --score-min "${analysis_type.alignment_options.align_mode.score_min_loc}"\n #end if\n #end if\n- \n+\n #if str( $analysis_type.scoring_options.scoring_options_selector ) == "yes":\n #if ( str( $analysis_type.alignment_options.alignment_options_selector ) == "yes" and str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "local" ):\n --ma "${analysis_type.scoring_options.ma}"\n@@ -142,36 +141,39 @@\n --rdg "${analysis_type.scoring_options.rdg_read_open},${analysis_type.scoring_options.rdg_read_extend}"\n --rfg "${analysis_type.scoring_options.rfg_ref_open},${analysis_type.scoring_options.rfg_ref_extend}"\n #end if\n- \n+\n #if str( $analysis_type.reporting_options.reporting_options_selector ) == "k":\n -k "${analysis_type.reporting_options.k}"\n #elif str( $analysis_type.reporting_options.reporting_options_selector ) == "a":\n -a\n #end if\n- \n+\n #if str( $analysis_type.effort_options.effort_options_selector ) == "yes":\n -D "${analysis_type.effort_options.D}"\n -R "${analysis_type.effort_options.R}"\n #end if\n- \n+\n #if str( $analysis_type.sam_options.sam_options_selector ) == "yes":\n ${analysis_type.sam_options.no_unal}\n ${analysis_type.sam_options.omit_sec_seq}\n #end if\n- \n+\n #if str( $analysis_type.other_options.other_options_selector ) == "yes":\n+ ${analysis_type.other_options.reorder}\n ${analysis_type.other_options.non_deterministic}\n --seed "${analysis_type.other_options.seed}"\n #end if\n- \n+\n #elif str( $analysis_type.analysis_type_selector ) == "cline":\n ${analysis_type.cline}\n #end if\n- \n- -S "galaxy_bowtie_2_output.sam" &&\n \n- ## view/sort and output BAM file\n- ( samtools view -Su "galaxy_bowtie_2_output.sam" | samtools sort -o - - > $output )\n+ ## output file\n+ #if ( str( $analysis_type.analysis_type_selector '..b'elp="By default, the output from this Bowtie2 wrapper is a sorted BAM file."/>\n </when>\n </conditional>\n </inputs>\n@@ -437,21 +440,66 @@\n <data format="fastqsanger" name="output_unaligned_reads_l" label="${tool.name} on ${on_string}: unaligned reads (L)" >\n <filter>library[\'unaligned_file\'] is True</filter>\n <actions>\n- <action type="format">\n- <option type="from_param" name="library.input_1" param_attribute="ext" />\n- </action>\n+ <conditional name="library.type">\n+ <when value="single">\n+ <action type="format">\n+ <option type="from_param" name="library.input_1" param_attribute="ext" />\n+ </action>\n+ </when>\n+ <when value="paired">\n+ <action type="format">\n+ <option type="from_param" name="library.input_1" param_attribute="ext" />\n+ </action>\n+ </when>\n+ <when value="paired_collection">\n+ <action type="format">\n+ <option type="from_param" name="library.input_1" param_attribute="forward.ext" />\n+ </action>\n+ </when>\n+ </conditional>\n </actions>\n </data>\n <data format="fastqsanger" name="output_unaligned_reads_r" label="${tool.name} on ${on_string}: unaligned reads (R)">\n <filter>( library[\'type\'] == "paired" or library[\'type\'] == "paired_collection" ) and library[\'unaligned_file\'] is True</filter>\n <actions>\n- <action type="format">\n- <option type="from_param" name="library.input_1" param_attribute="ext" />\n- </action>\n+ <conditional name="library.type">\n+ <when value="paired">\n+ <action type="format">\n+ <option type="from_param" name="library.input_2" param_attribute="ext" />\n+ </action>\n+ </when>\n+ <when value="paired_collection">\n+ <action type="format">\n+ <option type="from_param" name="library.input_1" param_attribute="reverse.ext" />\n+ </action>\n+ </when>\n+ </conditional>\n </actions>\n </data>\n \n <data format="bam" name="output" label="${tool.name} on ${on_string}: aligned reads (sorted BAM)">\n+ <filter>analysis_type[\'analysis_type_selector\'] == "simple" or analysis_type[\'sam_opt\'] is False</filter>\n+ <actions>\n+ <conditional name="reference_genome.source">\n+ <when value="indexed">\n+ <action type="metadata" name="dbkey">\n+ <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0">\n+ <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>\n+ <filter type="param_value" ref="reference_genome.index" column="0"/>\n+ </option>\n+ </action>\n+ </when>\n+ <when value="history">\n+ <action type="metadata" name="dbkey">\n+ <option type="from_param" name="reference_genome.own_file" param_attribute="dbkey" />\n+ </action>\n+ </when>\n+ </conditional>\n+ </actions>\n+ </data>\n+\n+ <data format="sam" name="output_sam" label="${tool.name} on ${on_string}: aligned reads (SAM)">\n+ <filter>analysis_type[\'analysis_type_selector\'] == "full" and analysis_type[\'sam_opt\'] is True</filter>\n <actions>\n <conditional name="reference_genome.source">\n <when value="indexed">\n' |
| b |
| diff -r e23b0cdeeba6 -r 4f92dccc808a read_group_macros.xml --- a/read_group_macros.xml Wed Aug 26 12:46:11 2015 -0400 +++ b/read_group_macros.xml Wed Nov 11 12:04:23 2015 -0500 |
| [ |
| @@ -121,7 +121,7 @@ #set $rg_pg = '' #end if - #if str($rg_param("PI")) + #if $rg_param("PI") != None #set $rg_pi = str($rg_param("PI")) #else #set $rg_pi = '' @@ -146,7 +146,7 @@ </when> </xml> <xml name="read_group_id_param"> - <param name="ID" type="text" value="" size="20" label="Read group identifier (ID)" help="This value must be unique among multiple samples in your experiment" optional="false"> + <param name="ID" type="text" value="" label="Read group identifier (ID)" help="This value must be unique among multiple samples in your experiment" optional="false"> <validator type="empty_field" /> </param> </xml> @@ -158,7 +158,7 @@ </conditional> </xml> <xml name="read_group_sm_param"> - <param name="SM" type="text" value="" size="20" label="Read group sample name (SM)" help="This value should be descriptive. Use pool name where a pool is being sequenced" /> + <param name="SM" type="text" value="" label="Read group sample name (SM)" help="This value should be descriptive. Use pool name where a pool is being sequenced" /> </xml> <xml name="read_group_sm_conditional"> <conditional name="read_group_sm_conditional"> @@ -171,7 +171,7 @@ as per Picard. --> <xml name="read_group_sm_param_required"> - <param name="SM" type="text" value="" size="20" label="Read group sample name (SM)" optional="false" help="This value should be descriptive. Use pool name where a pool is being sequenced"> + <param name="SM" type="text" value="" label="Read group sample name (SM)" optional="false" help="This value should be descriptive. Use pool name where a pool is being sequenced"> <validator type="empty_field" /> </param> </xml> @@ -194,7 +194,7 @@ </param> </xml> <xml name="read_group_lb_param"> - <param name="LB" type="text" size="25" label="Library name (LB)" optional="true" /> + <param name="LB" type="text" label="Library name (LB)" optional="true" /> </xml> <xml name="read_group_lb_conditional"> <conditional name="read_group_lb_conditional"> @@ -204,7 +204,7 @@ </conditional> </xml> <xml name="read_group_lb_required_param"> - <param name="LB" type="text" size="25" label="Library name (LB)" optional="false"> + <param name="LB" type="text" label="Library name (LB)" optional="false"> <validator type="empty_field" /> </param> </xml> @@ -216,33 +216,33 @@ </conditional> </xml> <xml name="read_group_cn_param"> - <param name="CN" type="text" size="25" label="Sequencing center that produced the read (CN)" /> + <param name="CN" type="text" label="Sequencing center that produced the read (CN)" /> </xml> <xml name="read_group_ds_param"> - <param name="DS" type="text" size="25" label="Description (DS)" /> + <param name="DS" type="text" label="Description (DS)" /> </xml> <xml name="read_group_dt_param"> - <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" /> + <param name="DT" type="text" label="Date that run was produced (DT)" help="ISO8601 format date or date/time, like YYYY-MM-DD" /> </xml> <xml name="read_group_fo_param"> - <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]+/"> + <param name="FO" type="text" 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]+/"> <validator type="regex" message="Invalid flow order">\*|[ACMGRSVTWYHKDBN]+$</validator> </param> </xml> <xml name="read_group_ks_param"> - <param name="KS" type="text" size="25" label="The array of nucleotide bases that correspond to the key sequence of each read (KS)" /> + <param name="KS" type="text" label="The array of nucleotide bases that correspond to the key sequence of each read (KS)" /> </xml> <xml name="read_group_pg_param"> - <param name="PG" type="text" size="25" label="Programs used for processing the read group (PG)" /> + <param name="PG" type="text" label="Programs used for processing the read group (PG)" /> </xml> <xml name="read_group_pi_param"> <param name="PI" type="integer" optional="true" label="Predicted median insert size (PI)" /> </xml> <xml name="read_group_pu_param"> - <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" /> + <param name="PU" type="text" label="Platform unit (PU)" help="Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)" optional="True" /> </xml> <xml name="read_group_pu_required_param"> - <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" /> + <param name="PU" type="text" label="Platform unit (PU)" help="Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)" optional="False" /> </xml> <!-- Only ID is required - all groups available --> <xml name="read_group_inputs_spec"> |