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Rework some duplication out tophat wrappers using macros. This dmeonstrates how macros can reduce duplication inside a file (e.g. the dbKeyActions macro) and between files (e.g. the own_junctionsConditional macro).

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This commit is contained in:
John Chilton
2013-02-23 14:09:53 -06:00
parent e9dc68f0a6
commit 05028a920f
4 changed files with 186 additions and 391 deletions
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tools/ngs_rna/tophat2_wrapper.xml
+34 -131
View File
@@ -143,23 +143,12 @@
</param>
</when>
</conditional>
<conditional name="refGenomeSource">
<param name="genomeSource" type="select" label="Use a built in reference genome or own from your history" help="Built-in genomes were created using default options">
<option value="indexed" selected="True">Use a built-in genome</option>
<option value="history">Use a genome from history</option>
</param>
<when value="indexed">
<param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
<options from_data_table="tophat2_indexes">
<filter type="sort_by" column="2"/>
<validator type="no_options" message="No genomes are available for the selected input dataset"/>
</options>
</param>
</when>
<when value="history">
<param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
</when> <!-- history -->
</conditional> <!-- refGenomeSource -->
<expand macro="refGenomeSourceConditional">
<options from_data_table="tophat2_indexes">
<filter type="sort_by" column="2"/>
<validator type="no_options" message="No genomes are available for the selected input dataset"/>
</options>
</expand>
<conditional name="params">
<param name="settingsType" type="select" label="TopHat settings to use" help="You can use the default settings or set custom values for any of Tophat's parameters.">
<option value="preSet">Use Defaults</option>
@@ -182,17 +171,7 @@
<param name="splice_mismatches" type="integer" value="0" label="Maximum number of mismatches that can appear in the anchor region of spliced alignment" />
<param name="min_intron_length" type="integer" value="70" label="The minimum intron length" help="TopHat will ignore donor/acceptor pairs closer than this many bases apart." />
<param name="max_intron_length" type="integer" value="500000" label="The maximum intron length" help="When searching for junctions ab initio, TopHat will ignore donor/acceptor pairs farther than this many bases apart, except when such a pair is supported by a split segment alignment of a long read." />
<conditional name="indel_search">
<param name="allow_indel_search" type="select" label="Allow indel search">
<option value="Yes">Yes</option>
<option value="No">No</option>
</param>
<when value="No"/>
<when value="Yes">
<param name="max_insertion_length" type="integer" value="3" label="Max insertion length." help="The maximum insertion length." />
<param name="max_deletion_length" type="integer" value="3" label="Max deletion length." help="The maximum deletion length." />
</when>
</conditional>
<expand macro="indel_searchConditional" />
alignments (number of reads divided by average depth of coverage)" help="0.0 to 1.0 (0 to turn off)" />
<param name="max_multihits" type="integer" value="20" label="Maximum number of alignments to be allowed" />
<param name="min_segment_intron" type="integer" value="50" label="Minimum intron length that may be found during split-segment (default) search" />
@@ -201,40 +180,7 @@
<param name="seg_length" type="integer" value="25" label="Minimum length of read segments" />
<!-- Options for supplying own junctions. -->
<conditional name="own_junctions">
<param name="use_junctions" type="select" label="Use Own Junctions">
<option value="No">No</option>
<option value="Yes">Yes</option>
</param>
<when value="Yes">
<conditional name="gene_model_ann">
<param name="use_annotations" type="select" label="Use Gene Annotation Model">
<option value="No">No</option>
<option value="Yes">Yes</option>
</param>
<when value="No" />
<when value="Yes">
<param format="gtf,gff3" name="gene_annotation_model" type="data" label="Gene Model Annotations" help="TopHat will use the exon records in this file to build a set of known splice junctions for each gene, and will attempt to align reads to these junctions even if they would not normally be covered by the initial mapping."/>
</when>
</conditional>
<conditional name="raw_juncs">
<param name="use_juncs" type="select" label="Use Raw Junctions">
<option value="No">No</option>
<option value="Yes">Yes</option>
</param>
<when value="No" />
<when value="Yes">
<param format="interval" name="raw_juncs" type="data" label="Raw Junctions" help="Supply TopHat with a list of raw junctions. Junctions are specified one per line, in a tab-delimited format. Records look like: [chrom] [left] [right] [+/-] left and right are zero-based coordinates, and specify the last character of the left sequenced to be spliced to the first character of the right sequence, inclusive."/>
</when>
</conditional>
<param name="no_novel_juncs" type="select" label="Only look for supplied junctions">
<option value="No">No</option>
<option value="Yes">Yes</option>
</param>
</when>
<when value="No" />
</conditional> <!-- /own_junctions -->
<expand macro="own_junctionsConditional" />
<!-- Coverage search. -->
<conditional name="coverage_search">
<param name="use_search" type="select" label="Use Coverage Search" help="Enables the coverage based search for junctions. Use when coverage search is disabled by default (such as for reads 75bp or longer), for maximum sensitivity.">
@@ -319,83 +265,40 @@
<filter>(params['settingsType'] == 'full' and params['fusion_search']['do_search'] == 'Yes')</filter>
</data>
<data format="bed" name="insertions" label="${tool.name} on ${on_string}: insertions" from_work_dir="tophat_out/insertions.bed">
<actions>
<conditional name="refGenomeSource.genomeSource">
<when value="indexed">
<action type="metadata" name="dbkey">
<option type="from_data_table" name="tophat2_indexes" column="1" offset="0">
<filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
<filter type="param_value" ref="refGenomeSource.index" column="0"/>
</option>
</action>
</when>
<when value="history">
<action type="metadata" name="dbkey">
<option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
</action>
</when>
</conditional>
</actions>
<expand macro="dbKeyActions" />
</data>
<data format="bed" name="deletions" label="${tool.name} on ${on_string}: deletions" from_work_dir="tophat_out/deletions.bed">
<actions>
<conditional name="refGenomeSource.genomeSource">
<when value="indexed">
<action type="metadata" name="dbkey">
<option type="from_data_table" name="tophat2_indexes" column="1" offset="0">
<filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
<filter type="param_value" ref="refGenomeSource.index" column="0"/>
</option>
</action>
</when>
<when value="history">
<action type="metadata" name="dbkey">
<option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
</action>
</when>
</conditional>
</actions>
<expand macro="dbKeyActions" />
</data>
<data format="bed" name="junctions" label="${tool.name} on ${on_string}: splice junctions" from_work_dir="tophat_out/junctions.bed">
<actions>
<conditional name="refGenomeSource.genomeSource">
<when value="indexed">
<action type="metadata" name="dbkey">
<option type="from_data_table" name="tophat2_indexes" column="1" offset="0">
<filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
<filter type="param_value" ref="refGenomeSource.index" column="0"/>
</option>
</action>
</when>
<when value="history">
<action type="metadata" name="dbkey">
<option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
</action>
</when>
</conditional>
</actions>
<expand macro="dbKeyActions" />
</data>
<data format="bam" name="accepted_hits" label="${tool.name} on ${on_string}: accepted_hits" from_work_dir="tophat_out/accepted_hits.bam">
<actions>
<conditional name="refGenomeSource.genomeSource">
<when value="indexed">
<action type="metadata" name="dbkey">
<option type="from_data_table" name="tophat2_indexes" column="1" offset="0">
<filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
<filter type="param_value" ref="refGenomeSource.index" column="0"/>
</option>
</action>
</when>
<when value="history">
<action type="metadata" name="dbkey">
<option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
</action>
</when>
</conditional>
</actions>
<expand macro="dbKeyActions" />
</data>
</outputs>
<macros>
<import>tophat_macros.xml</import>
<macro name="dbKeyActions">
<actions>
<conditional name="refGenomeSource.genomeSource">
<when value="indexed">
<action type="metadata" name="dbkey">
<option type="from_data_table" name="tophat2_indexes" column="1" offset="0">
<filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
<filter type="param_value" ref="refGenomeSource.index" column="0"/>
</option>
</action>
</when>
<when value="history">
<action type="metadata" name="dbkey">
<option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
</action>
</when>
</conditional>
</actions>
</macro>
</macros>
<tests>
<!-- Test base-space single-end reads with pre-built index and preset parameters -->
<test>
tools/ngs_rna/tophat_color_wrapper.xml
+46 -129
View File
@@ -154,23 +154,12 @@
</command>
<inputs>
<param format="fastqcssanger" name="input1" type="data" label="RNA-Seq FASTQ file" help="Color-space: Must have Sanger-scaled quality values with ASCII offset 33" />
<conditional name="refGenomeSource">
<param name="genomeSource" 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">
<option value="indexed">Use a built-in index</option>
<option value="history">Use one from the history</option>
</param>
<when value="indexed">
<param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
<options from_data_table="tophat_indexes_color">
<filter type="sort_by" column="2"/>
<validator type="no_options" message="No indexes are available for the selected input dataset"/>
</options>
</param>
</when>
<when value="history">
<param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
</when> <!-- history -->
</conditional> <!-- refGenomeSource -->
<expand macro="refGenomeSourceConditional">
<options from_data_table="tophat_indexes_color">
<filter type="sort_by" column="2"/>
<validator type="no_options" message="No indexes are available for the selected input dataset"/>
</options>
</expand>
<conditional name="singlePaired">
<param name="sPaired" type="select" label="Is this library mate-paired?">
<option value="single">Single-end</option>
@@ -194,17 +183,7 @@
<param name="splice_mismatches" type="integer" value="0" label="Maximum number of mismatches that can appear in the anchor region of spliced alignment" />
<param name="min_intron_length" type="integer" value="70" label="The minimum intron length" help="TopHat will ignore donor/acceptor pairs closer than this many bases apart." />
<param name="max_intron_length" type="integer" value="500000" label="The maximum intron length" help="When searching for junctions ab initio, TopHat will ignore donor/acceptor pairs farther than this many bases apart, except when such a pair is supported by a split segment alignment of a long read." />
<conditional name="indel_search">
<param name="allow_indel_search" type="select" label="Allow indel search">
<option value="Yes">Yes</option>
<option value="No">No</option>
</param>
<when value="No"/>
<when value="Yes">
<param name="max_insertion_length" type="integer" value="3" label="Max insertion length." help="The maximum insertion length." />
<param name="max_deletion_length" type="integer" value="3" label="Max deletion length." help="The maximum deletion length." />
</when>
</conditional>
<expand macro="indel_searchConditional" />
<param name="junction_filter" type="float" value="0.15" label="Minimum isoform fraction: filter out junctions supported by too few alignments (number of reads divided by average depth of coverage)" help="0.0 to 1.0 (0 to turn off)" />
<param name="max_multihits" type="integer" value="40" label="Maximum number of alignments to be allowed" />
<param name="min_segment_intron" type="integer" value="50" label="Minimum intron length that may be found during split-segment (default) search" />
@@ -230,20 +209,8 @@
<param format="gtf" name="gene_annotation_model" type="data" label="Gene Model Annotations" help="TopHat will use the exon records in this file to build a set of known splice junctions for each gene, and will attempt to align reads to these junctions even if they would not normally be covered by the initial mapping."/>
</when>
</conditional>
<conditional name="raw_juncs">
<param name="use_juncs" type="select" label="Use Raw Junctions">
<option value="No">No</option>
<option value="Yes">Yes</option>
</param>
<when value="No" />
<when value="Yes">
<param format="interval" name="raw_juncs" type="data" label="Raw Junctions" help="Supply TopHat with a list of raw junctions. Junctions are specified one per line, in a tab-delimited format. Records look like: [chrom] [left] [right] [+/-] left and right are zero-based coordinates, and specify the last character of the left sequenced to be spliced to the first character of the right sequence, inclusive."/>
</when>
</conditional>
<param name="no_novel_juncs" type="select" label="Only look for supplied junctions">
<option value="No">No</option>
<option value="Yes">Yes</option>
</param>
<expand macro="raw_juncsConditional" />
<expand macro="no_novel_juncsParam" />
</when>
<when value="No" />
</conditional> <!-- /own_junctions -->
@@ -301,17 +268,7 @@
<param name="splice_mismatches" type="integer" value="0" label="Maximum number of mismatches that can appear in the anchor region of spliced alignment" />
<param name="min_intron_length" type="integer" value="70" label="The minimum intron length" help="TopHat will ignore donor/acceptor pairs closer than this many bases apart." />
<param name="max_intron_length" type="integer" value="500000" label="The maximum intron length" help="When searching for junctions ab initio, TopHat will ignore donor/acceptor pairs farther than this many bases apart, except when such a pair is supported by a split segment alignment of a long read." />
<conditional name="indel_search">
<param name="allow_indel_search" type="select" label="Allow indel search">
<option value="Yes">Yes</option>
<option value="No">No</option>
</param>
<when value="No"/>
<when value="Yes">
<param name="max_insertion_length" type="integer" value="3" label="Max insertion length." help="The maximum insertion length." />
<param name="max_deletion_length" type="integer" value="3" label="Max deletion length." help="The maximum deletion length." />
</when>
</conditional>
<expand macro="indel_searchConditional" />
<param name="junction_filter" type="float" value="0.15" label="Minimum isoform fraction: filter out junctions supported by too few alignments (number of reads divided by average depth of coverage)" help="0.0 to 1.0 (0 to turn off)" />
<param name="max_multihits" type="integer" value="40" label="Maximum number of alignments to be allowed" />
<param name="min_segment_intron" type="integer" value="50" label="Minimum intron length that may be found during split-segment (default) search" />
@@ -399,90 +356,50 @@
( singlePaired['pParams']['indel_search']['allow_indel_search'] == 'Yes' ) )
)
</filter>
<actions>
<conditional name="refGenomeSource.genomeSource">
<when value="indexed">
<action type="metadata" name="dbkey">
<option type="from_data_table" name="tophat_indexes_color" column="1" offset="0">
<filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
<filter type="param_value" ref="refGenomeSource.index" column="0"/>
</option>
</action>
</when>
<when value="history">
<action type="metadata" name="dbkey">
<option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
</action>
</when>
</conditional>
</actions>
<expand macro="dbKeyActions" />
</data>
<data format="bed" name="deletions" label="${tool.name} on ${on_string}: deletions" from_work_dir="tophat_out/deletions.bed">
<filter>
<expand macro="dbKeyActions" />
</data>
<data format="bed" name="junctions" label="${tool.name} on ${on_string}: splice junctions">
<expand macro="dbKeyActions" />
</data>
<data format="bam" name="accepted_hits" label="${tool.name} on ${on_string}: accepted_hits">
<expand macro="dbKeyActions" />
</data>
</outputs>
<macros>
<import>tophat_macros.xml</import>
<macro name="bedFilter">
<filter>
(
( ( 'sParams' in singlePaired ) and ( 'indel_search' in singlePaired['sParams'] ) and
( singlePaired['sParams']['indel_search']['allow_indel_search'] == 'Yes' ) ) or
( ( 'pParams' in singlePaired ) and ( 'indel_search' in singlePaired['pParams'] ) and
( singlePaired['pParams']['indel_search']['allow_indel_search'] == 'Yes' ) )
)
</filter>
<actions>
<conditional name="refGenomeSource.genomeSource">
<when value="indexed">
<action type="metadata" name="dbkey">
<option type="from_data_table" name="tophat_indexes_color" column="1" offset="0">
<filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
<filter type="param_value" ref="refGenomeSource.index" column="0"/>
</option>
</action>
</when>
<when value="history">
<action type="metadata" name="dbkey">
<option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
</action>
</when>
</conditional>
</actions>
</data>
<data format="bed" name="junctions" label="${tool.name} on ${on_string}: splice junctions">
<actions>
<conditional name="refGenomeSource.genomeSource">
<when value="indexed">
<action type="metadata" name="dbkey">
<option type="from_data_table" name="tophat_indexes_color" column="1" offset="0">
<filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
<filter type="param_value" ref="refGenomeSource.index" column="0"/>
</option>
</action>
</when>
<when value="history">
<action type="metadata" name="dbkey">
<option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
</action>
</when>
</conditional>
</actions>
</data>
<data format="bam" name="accepted_hits" label="${tool.name} on ${on_string}: accepted_hits">
<actions>
<conditional name="refGenomeSource.genomeSource">
<when value="indexed">
<action type="metadata" name="dbkey">
<option type="from_data_table" name="tophat_indexes_color" column="1" offset="0">
<filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
<filter type="param_value" ref="refGenomeSource.index" column="0"/>
</option>
</action>
</when>
<when value="history">
<action type="metadata" name="dbkey">
<option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
</action>
</when>
</conditional>
</actions>
</data>
</outputs>
</filter>
</macro>
<macro name="dbKeyActions">
<actions>
<conditional name="refGenomeSource.genomeSource">
<when value="indexed">
<action type="metadata" name="dbkey">
<option type="from_data_table" name="tophat_indexes_color" column="1" offset="0">
<filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
<filter type="param_value" ref="refGenomeSource.index" column="0"/>
</option>
</action>
</when>
<when value="history">
<action type="metadata" name="dbkey">
<option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
</action>
</when>
</conditional>
</actions>
</macro>
</macros>
<tests>
<!-- Test color-space single-end reads with user-supplied reference fasta and preset parameters -->
<test>
tools/ngs_rna/tophat_macros.xml
+72
View File
@@ -0,0 +1,72 @@
<macros>
<macro name="refGenomeSourceConditional">
<conditional name="refGenomeSource">
<param name="genomeSource" type="select" label="Use a built in reference genome or own from your history" help="Built-ins genomes were created using default options">
<option value="indexed" selected="True">Use a built-in genome</option>
<option value="history">Use a genome from history</option>
</param>
<when value="indexed">
<param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
<yield />
</param>
</when>
<when value="history">
<param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
</when> <!-- history -->
</conditional> <!-- refGenomeSource -->
</macro>
<macro name="indel_searchConditional">
<conditional name="indel_search">
<param name="allow_indel_search" type="select" label="Allow indel search">
<option value="Yes">Yes</option>
<option value="No">No</option>
</param>
<when value="No"/>
<when value="Yes">
<param name="max_insertion_length" type="integer" value="3" label="Max insertion length." help="The maximum insertion length." />
<param name="max_deletion_length" type="integer" value="3" label="Max deletion length." help="The maximum deletion length." />
</when>
</conditional>
</macro>
<macro name="own_junctionsConditional">
<conditional name="own_junctions">
<param name="use_junctions" type="select" label="Use Own Junctions">
<option value="No">No</option>
<option value="Yes">Yes</option>
</param>
<when value="Yes">
<conditional name="gene_model_ann">
<param name="use_annotations" type="select" label="Use Gene Annotation Model">
<option value="No">No</option>
<option value="Yes">Yes</option>
</param>
<when value="No" />
<when value="Yes">
<param format="gtf,gff3" name="gene_annotation_model" type="data" label="Gene Model Annotations" help="TopHat will use the exon records in this file to build a set of known splice junctions for each gene, and will attempt to align reads to these junctions even if they would not normally be covered by the initial mapping."/>
</when>
</conditional>
<expand macro="raw_juncsConditional" />
<expand macro="no_novel_juncsParam" />
</when>
<when value="No" />
</conditional> <!-- /own_junctions -->
</macro>
<macro name="raw_juncsConditional">
<conditional name="raw_juncs">
<param name="use_juncs" type="select" label="Use Raw Junctions">
<option value="No">No</option>
<option value="Yes">Yes</option>
</param>
<when value="No" />
<when value="Yes">
<param format="interval" name="raw_juncs" type="data" label="Raw Junctions" help="Supply TopHat with a list of raw junctions. Junctions are specified one per line, in a tab-delimited format. Records look like: [chrom] [left] [right] [+/-] left and right are zero-based coordinates, and specify the last character of the left sequenced to be spliced to the first character of the right sequence, inclusive."/>
</when>
</conditional>
</macro>
<macro name="no_novel_juncsParam">
<param name="no_novel_juncs" type="select" label="Only look for supplied junctions">
<option value="No">No</option>
<option value="Yes">Yes</option>
</param>
</macro>
</macros>
tools/ngs_rna/tophat_wrapper.xml
+34 -131
View File
@@ -151,23 +151,12 @@
</command>
<inputs>
<param format="fastqsanger" name="input1" type="data" label="RNA-Seq FASTQ file" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33" />
<conditional name="refGenomeSource">
<param name="genomeSource" type="select" label="Use a built in reference genome or own from your history" help="Built-ins genomes were created using default options">
<option value="indexed" selected="True">Use a built-in genome</option>
<option value="history">Use a genome from history</option>
</param>
<when value="indexed">
<param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
<options from_data_table="tophat_indexes">
<filter type="sort_by" column="2"/>
<validator type="no_options" message="No genomes are available for the selected input dataset"/>
</options>
</param>
</when>
<when value="history">
<param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
</when> <!-- history -->
</conditional> <!-- refGenomeSource -->
<expand macro="refGenomeSourceConditional">
<options from_data_table="tophat_indexes">
<filter type="sort_by" column="2"/>
<validator type="no_options" message="No genomes are available for the selected input dataset"/>
</options>
</expand>
<conditional name="singlePaired">
<param name="sPaired" type="select" label="Is this library mate-paired?">
<option value="single">Single-end</option>
@@ -298,17 +287,7 @@ alignments (number of reads divided by average depth of coverage)" help="0.0 to
<param name="splice_mismatches" type="integer" value="0" label="Maximum number of mismatches that can appear in the anchor region of spliced alignment" />
<param name="min_intron_length" type="integer" value="70" label="The minimum intron length" help="TopHat will ignore donor/acceptor pairs closer than this many bases apart." />
<param name="max_intron_length" type="integer" value="500000" label="The maximum intron length" help="When searching for junctions ab initio, TopHat will ignore donor/acceptor pairs farther than this many bases apart, except when such a pair is supported by a split segment alignment of a long read." />
<conditional name="indel_search">
<param name="allow_indel_search" type="select" label="Allow indel search">
<option value="Yes">Yes</option>
<option value="No">No</option>
</param>
<when value="No"/>
<when value="Yes">
<param name="max_insertion_length" type="integer" value="3" label="Max insertion length." help="The maximum insertion length." />
<param name="max_deletion_length" type="integer" value="3" label="Max deletion length." help="The maximum deletion length." />
</when>
</conditional>
<expand macro="indel_searchConditional" />
<param name="max_multihits" type="integer" value="20" label="Maximum number of alignments to be allowed" />
<param name="min_segment_intron" type="integer" value="50" label="Minimum intron length that may be found during split-segment (default) search" />
<param name="max_segment_intron" type="integer" value="500000" label="Maximum intron length that may be found during split-segment (default) search" />
@@ -316,40 +295,7 @@ alignments (number of reads divided by average depth of coverage)" help="0.0 to
<param name="seg_mismatches" type="integer" min="0" max="3" value="2" label="Number of mismatches allowed in each segment alignment for reads mapped independently" />
<param name="seg_length" type="integer" value="25" label="Minimum length of read segments" />
<!-- Options for supplying own junctions. -->
<conditional name="own_junctions">
<param name="use_junctions" type="select" label="Use Own Junctions">
<option value="No">No</option>
<option value="Yes">Yes</option>
</param>
<when value="Yes">
<conditional name="gene_model_ann">
<param name="use_annotations" type="select" label="Use Gene Annotation Model">
<option value="No">No</option>
<option value="Yes">Yes</option>
</param>
<when value="No" />
<when value="Yes">
<param format="gtf" name="gene_annotation_model" type="data" label="Gene Model Annotations" help="TopHat will use the exon records in this file to build a set of known splice junctions for each gene, and will attempt to align reads to these junctions even if they would not normally be covered by the initial mapping."/>
</when>
</conditional>
<conditional name="raw_juncs">
<param name="use_juncs" type="select" label="Use Raw Junctions">
<option value="No">No</option>
<option value="Yes">Yes</option>
</param>
<when value="No" />
<when value="Yes">
<param format="interval" name="raw_juncs" type="data" label="Raw Junctions" help="Supply TopHat with a list of raw junctions. Junctions are specified one per line, in a tab-delimited format. Records look like: [chrom] [left] [right] [+/-] left and right are zero-based coordinates, and specify the last character of the left sequenced to be spliced to the first character of the right sequence, inclusive."/>
</when>
</conditional>
<param name="no_novel_juncs" type="select" label="Only look for supplied junctions">
<option value="No">No</option>
<option value="Yes">Yes</option>
</param>
</when>
<when value="No" />
</conditional> <!-- /own_junctions -->
<expand macro="own_junctionsConditional" />
<!-- Closure search. -->
<conditional name="closure_search">
<param name="use_search" type="select" label="Use Closure Search">
@@ -387,83 +333,40 @@ alignments (number of reads divided by average depth of coverage)" help="0.0 to
<outputs>
<data format="bed" name="insertions" label="${tool.name} on ${on_string}: insertions" from_work_dir="tophat_out/insertions.bed">
<actions>
<conditional name="refGenomeSource.genomeSource">
<when value="indexed">
<action type="metadata" name="dbkey">
<option type="from_data_table" name="tophat_indexes" column="1" offset="0">
<filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
<filter type="param_value" ref="refGenomeSource.index" column="0"/>
</option>
</action>
</when>
<when value="history">
<action type="metadata" name="dbkey">
<option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
</action>
</when>
</conditional>
</actions>
<expand macro="dbKeyActions" />
</data>
<data format="bed" name="deletions" label="${tool.name} on ${on_string}: deletions" from_work_dir="tophat_out/deletions.bed">
<actions>
<conditional name="refGenomeSource.genomeSource">
<when value="indexed">
<action type="metadata" name="dbkey">
<option type="from_data_table" name="tophat_indexes" column="1" offset="0">
<filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
<filter type="param_value" ref="refGenomeSource.index" column="0"/>
</option>
</action>
</when>
<when value="history">
<action type="metadata" name="dbkey">
<option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
</action>
</when>
</conditional>
</actions>
<expand macro="dbKeyActions" />
</data>
<data format="bed" name="junctions" label="${tool.name} on ${on_string}: splice junctions" from_work_dir="tophat_out/junctions.bed">
<actions>
<conditional name="refGenomeSource.genomeSource">
<when value="indexed">
<action type="metadata" name="dbkey">
<option type="from_data_table" name="tophat_indexes" column="1" offset="0">
<filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
<filter type="param_value" ref="refGenomeSource.index" column="0"/>
</option>
</action>
</when>
<when value="history">
<action type="metadata" name="dbkey">
<option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
</action>
</when>
</conditional>
</actions>
<expand macro="dbKeyActions" />
</data>
<data format="bam" name="accepted_hits" label="${tool.name} on ${on_string}: accepted_hits" from_work_dir="tophat_out/accepted_hits.bam">
<actions>
<conditional name="refGenomeSource.genomeSource">
<when value="indexed">
<action type="metadata" name="dbkey">
<option type="from_data_table" name="tophat_indexes" column="1" offset="0">
<filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
<filter type="param_value" ref="refGenomeSource.index" column="0"/>
</option>
</action>
</when>
<when value="history">
<action type="metadata" name="dbkey">
<option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
</action>
</when>
</conditional>
</actions>
<expand macro="dbKeyActions" />
</data>
</outputs>
<macros>
<import>tophat_macros.xml</import>
<macro name="dbKeyActions">
<actions>
<conditional name="refGenomeSource.genomeSource">
<when value="indexed">
<action type="metadata" name="dbkey">
<option type="from_data_table" name="tophat_indexes" column="1" offset="0">
<filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
<filter type="param_value" ref="refGenomeSource.index" column="0"/>
</option>
</action>
</when>
<when value="history">
<action type="metadata" name="dbkey">
<option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
</action>
</when>
</conditional>
</actions>
</macro>
</macros>
<tests>
<!-- Test base-space single-end reads with pre-built index and preset parameters -->
<test>