Mercurial > repos > iuc > circexplorer2
diff circexplorer2.xml @ 0:465d6578b4d0 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2 commit fe03991cd7c43f5266314d1fb9e4108f1ab102e8
| author | iuc |
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| date | Fri, 26 Aug 2022 22:43:38 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/circexplorer2.xml Fri Aug 26 22:43:38 2022 +0000 @@ -0,0 +1,408 @@ +<tool id="circexplorer2" name="CIRCexplorer2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> + <description>circular RNA analysis</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro='xrefs'/> + <command detect_errors="exit_code"><![CDATA[ + #if $mode.selector == 'align' + mkdir -p reads && + #set file_paths = [] + #for $i,$input_file in enumerate($mode.fastq) + #set $fname = 'file' + str($i) + "." + $input_file.ext + #set $file_path = 'reads/' + $fname + ln -s '$input_file' '$file_path' && + $file_paths.append($file_path) + #end for + CIRCexplorer2 align + @threads@ + --gtf '$mode.gtf' + -g '$mode.genome' + --fastq #echo ','.join($file_paths)# + $mode.bw + $mode.scale + $mode.skip_tophat + $mode.skip_tophat_fusion + && tar -zcvf alignment.tgz './alignment' + #else if $mode.selector == 'parse' + CIRCexplorer2 parse + -t $mode.aligner.selector + $mode.aligner.fusion_file + #if $mode.aligner.selector == 'TopHat-Fusion' + $mode.aligner.pe + #end if + $mode.aligner.f + #else if $mode.selector == 'annotate' + ln -s $mode.genome reference_genome.fa && + CIRCexplorer2 annotate + -r $mode.ref + -g reference_genome.fa + -b $mode.bed + $mode.no_fix + $mode.low_confidence + #else if $mode.selector == 'assemble' + tar -zxf $mode.tophat && + CIRCexplorer2 assemble + @threads@ + -r $mode.ref + -m ./alignment + $mode.remove_rRNA + && tar -zcvf assemble.tgz './assemble' + #else + ln -s '$mode.genome' reference_genome.fa && + #if $mode.assemble_file.ext.endswith(".gz") + tar -zxf $mode.assemble_file && + #else + tar -xf $mode.assemble_file && + #end if + #if $mode.as_option.selector == 'enabled' + tar -zxf $mode.as_option.tophat && + #end if + CIRCexplorer2 denovo + -d ./assemble + -r $mode.ref + -b $mode.bed + -g reference_genome.fa + #if $mode.abs + --abs 'abs' + #end if + #if $mode.as_option.selector == 'enabled' + --as 'as' + $mode.as_option.type_mapping './alignment' + #end if + $mode.no_fix + $mode.rpkm + #end if + ]]></command> + <inputs> + <conditional name="mode"> + <param name="selector" type="select" + label="Tool module" help="CIRCexplorer2 contains 5 modules. Each module + functions as an independent component owning its distinctive duty. + Meanwhile, they inteact with each other, and different circular RNA + analysis pipelines are derived from different combinations of several + modules."> + <option value="align">Align: Map circular RNA junction reads with TopHat2/TopHat-Fusion</option> + <option value="parse">Parse: Parse fusion junction information from other aligners</option> + <option value="annotate">Annotate: Annotate circular RNA junction reads with gene annotations</option> + <option value="assemble">Assemble: Assemble transcriptome for circular RNAs</option> + <option value="denovo">De novo: Fetch de novo circular RNA isoforms</option> + </param> + <when value="align"> + <param argument="--gtf" type="data" format="gtf" label="Annotation GTF file" /> + <expand macro="genome_file"/> + <param argument="--fastq" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" multiple="true" label="RNA-seq FASTQ file(s)" + help="Only single-read RNA-seq is supported. It is recommended to convert paired-end RNA-seq to single-read RNA-seq before alignment"/> + <param argument="--bw" type="boolean" truevalue="--bw" falsevalue="" checked="false" + label="Create BigWig file" help=" It will not consider strand information of read alignment"/> + <param argument="--scale" type="boolean" truevalue="--scale" falsevalue="" checked="false" + label="Scale BigWig to HPB" help="Expression levels will be scaled to hits per billion-mapped-bases (HPB)" /> + <param argument="--skip-tophat" type="boolean" truevalue="--skip-tophat" falsevalue="" checked="false" + label="Skip TopHat mapping" help="CIRexplorer2 aligns reads onto genome and transcriptome using TopHat2 to + reduce false positive reads aligned in the TopHat-Fusion alignment step" /> + <param argument="--skip-tophat-fusion" type="boolean" truevalue="--skip-tophat-fusion" falsevalue="" checked="false" + label="Skip TopHat fusion" help="It is useful for poly(A)+ RNA-seq" /> + </when> + <when value="parse"> + <conditional name="aligner"> + <param argument="-t" name="selector" type="select" label="Aligner" + help="CIRCexplorer2 parse could accept results derived from TopHat-Fusion, + STAR, MapSplice, BWA and segemehl."> + <option value="TopHat-Fusion">TopHat-Fusion</option> + <option value="STAR">STAR</option> + <option value="MapSplice">MapSplice</option> + <option value="BWA">BWA</option> + <option value="segemehl">segemehl</option> + </param> + <when value="TopHat-Fusion"> + <expand macro="parse_fusion" format="bam" label="TopHat-Fusion file" + help="The required input file is accepted_hits.bam"/> + <expand macro="parse_statistics"/> + <param argument="--pe" type="boolean" truevalue="--pe" falsevalue="" checked="false" label="Paired-end aligner file" + help="Parse paired-end alignment file. If this is set, then -f is set automatically." /> + </when> + <when value="STAR"> + <expand macro="parse_fusion" format="interval,tabular" label="STAR fusion file" + help="The required input file is Chimeric.out.junction"/> + <expand macro="parse_statistics"/> + </when> + <when value="MapSplice"> + <expand macro="parse_fusion" format="txt" label="MapSplice fusion file" + help="The required input file is fusions_raw.txt"/> + <expand macro="parse_statistics"/> + </when> + <when value="BWA"> + <expand macro="parse_fusion" format="sam" label="BWA fusion file" + help="The required input file is the output sam file"/> + <expand macro="parse_statistics"/> + </when> + <when value="segemehl"> + <expand macro="parse_fusion" format="bed" label="segemehl fusion file" + help="The required input file is splicesites.bed"/> + <expand macro="parse_statistics"/> + </when> + </conditional> + </when> + <when value="annotate"> + <expand macro="annotation_file"/> + <expand macro="genome_file"/> + <expand macro="junction_file"/> + <param argument="--no-fix" type="boolean" truevalue="--no-fix" falsevalue="" checked="false" label="No fix mode" + help="When enabled, realignment step of fusion junction reads will be skipped. It is useful for species with + poor gene annotations, but the accuracy of circular RNA prediction would decrease." /> + <param argument="--low-confidence" type="boolean" truevalue="--low-confidence" falsevalue="" checked="false" label="Low confidence" + help="By default, it extracts fusion junction reads exactly matching the boundaries of exons of the same isoform by default. + If you set the --low-confidence, it will also extract fusion junction reads matching the boundaries of exons of the different + isofoms of the same gene" /> + </when> + <when value="assemble"> + <expand macro="annotation_file"/> + <expand macro="tophat_file"/> + <param argument="--remove-rRNA" type="boolean" truevalue="--remove-rRNA" falsevalue="" checked="false" + label="Remove rRNA" help="Ignore rRNA during assembling (only for human hg19)" /> + </when> + <when value="denovo"> + <expand macro="annotation_file"/> + <expand macro="junction_file"/> + <expand macro="genome_file"/> + <param name="assemble_file" type="data" format="tgz,tar" label="Assemble file" + help="Generated by the module CIRCexplorer2 assemble" /> + <param argument="--abs" type="boolean" truevalue="--abs" falsevalue="" checked="false" + label="Detect alternative back-splicing" help="When set, it will characterize the + alternative back-splicing of circular RNAs" /> + <conditional name="as_option"> + <param name="selector" type="select" label="Characterize alternative splicing of cirRNAs" + help="If enabled, it will characterize the alternative splicing of circular RNAs, including + cassette exons, retained introns, A5SS and A3SS"> + <option value="disabled">Disabled</option> + <option value="enabled">Enabled</option> + </param> + <when value="disabled"/> + <when value="enabled"> + <expand macro="tophat_file"/> + <param name="type_mapping" type="select" label="Type of mapping" + help="In this mode, you should also offer the path of TopHat mapping directory for + p(A)-/p(A)+ RNA-seq via -m/-n option"> + <option value="-m">p(A)-</option> + <option value="-n">p(A)+ RNA-seq</option> + </param> + </when> + </conditional> + <param argument="--no-fix" type="boolean" truevalue="--no-fix" falsevalue="" checked="false" label="No-fix mode" + help="If enabled, realignment step of fusion junction reads will be skipped. It is useful for species with + poor gene annotations, but the accuracy of circular RNA prediction would decrease." /> + <param argument="--rpkm" type="boolean" truevalue="--rpkm" falsevalue="" checked="false" label="Calculate RPKM for cassete exons" + help="If enabled, RPKM of cassette exons would be calculated" /> + </when> + </conditional> + </inputs> + <outputs> + <data name="alignment" format="tgz" from_work_dir="alignment.tgz" label="${tool.name} on ${on_string}: alignment file "> + <filter>mode['selector'] == 'align'</filter> + </data> + <data name="fusion_junction_bw" format="bigwig" from_work_dir="./alignment/tophat/accepted_hits.bw" label="${tool.name} on ${on_string}: BigWig"> + <filter>mode['selector'] == 'align'</filter> + <filter>mode['bw']</filter> + </data> + <data name="parse" format="bed" from_work_dir="back_spliced_junction.bed" label="${tool.name} on ${on_string}: back spliced junction (BED)"> + <filter>mode['selector'] == 'parse'</filter> + </data> + <data name="annotate" format="tabular" from_work_dir="circularRNA_known.txt" label="${tool.name} on ${on_string}: circRNA known"> + <filter>mode['selector'] == 'annotate'</filter> + </data> + <data name="annotate_low" format="tabular" from_work_dir="low_conf_circularRNA_known.txt" label="${tool.name} on ${on_string}: Low confidence circRNA"> + <filter>mode['selector'] == 'annotate'</filter> + <filter>mode['low_confidence']</filter> + </data> + <data name="assemble" format="tgz" from_work_dir="assemble.tgz" label="${tool.name} on ${on_string}: assemble file"> + <filter>mode['selector'] == 'assemble'</filter> + </data> + <data name="denovo_combined" format="tabular" from_work_dir="./denovo/combined_ref.txt" label="${tool.name} on ${on_string}: combined ref"> + <filter>mode['selector'] == 'denovo'</filter> + </data> + <data name="denovo_circularRNA" format="tabular" from_work_dir="./denovo/circularRNA_full.txt" label="${tool.name} on ${on_string}: circRNA full"> + <filter>mode['selector'] == 'denovo'</filter> + </data> + <data name="denovo_annotated" format="tabular" from_work_dir="./denovo/annotated_circ.txt" label="${tool.name} on ${on_string}: annotated circRNA"> + <filter>mode['selector'] == 'denovo'</filter> + </data> + <data name="denovo_novel" format="tabular" from_work_dir="./denovo/novel_circ.txt" label="${tool.name} on ${on_string}: novel circRNA"> + <filter>mode['selector'] == 'denovo'</filter> + </data> + <data name="denovo_abs5" format="tabular" from_work_dir="./abs/a5bs.txt" label="${tool.name} on ${on_string}: a5bs"> + <filter>mode['selector'] == 'denovo'</filter> + <filter>mode['abs']</filter> + </data> + <data name="denovo_abs3" format="tabular" from_work_dir="./abs/a3bs.txt" label="${tool.name} on ${on_string}: a3bs"> + <filter>mode['selector'] == 'denovo'</filter> + <filter>mode['abs']</filter> + </data> + <data name="denovo_all_exon" format="tabular" from_work_dir="./as/all_exon_info.txt" label="${tool.name} on ${on_string}: all exon info"> + <filter>mode['selector'] == 'denovo'</filter> + <filter>mode['as_option'] == 'enabled'</filter> + </data> + <data name="denovo_all_intron" format="tabular" from_work_dir="./as/all_intron_info.txt" label="${tool.name} on ${on_string}: all intron info"> + <filter>mode['selector'] == 'denovo'</filter> + <filter>mode['as_option'] == 'enabled'</filter> + </data> + <data name="denovo_a5ss" format="tabular" from_work_dir="./as/all_A5SS_info.txt" label="${tool.name} on ${on_string}: all A5SS info"> + <filter>mode['selector'] == 'denovo'</filter> + <filter>mode['as_option'] == 'enabled'</filter> + </data> + <data name="denovo_a3ss" format="tabular" from_work_dir="./as/all_A3SS_info.txt" label="${tool.name} on ${on_string}: all A3SS info"> + <filter>mode['selector'] == 'denovo'</filter> + <filter>mode['as_option'] == 'enabled'</filter> + </data> + </outputs> + <tests> + <test expect_num_outputs="1"> + <!--Test 01: Module align default options--> + <conditional name="mode"> + <param name="selector" value="align"/> + <param name="gtf" value="annotation_01.gtf"/> + <param name="genome" value="reference_01.fa"/> + <param name="fastq" value="reads_01.fastq,reads_02.fastq,reads_03.fastq"/> + <param name="skip_tophat_fusion" value="true"/> + </conditional> + <output name="alignment"> + <assert_contents> + <has_size value="3426053" delta="5000"/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <!--Test 02: Module align compressed files--> + <conditional name="mode"> + <param name="selector" value="align"/> + <param name="gtf" value="annotation_01.gtf"/> + <param name="genome" value="reference_01.fa"/> + <param name="fastq" value="reads_01.fastq.gz,reads_02.fastq.gz,reads_03.fastq.gz"/> + <param name="skip_tophat_fusion" value="true"/> + <param name="bw" value="true"/> + <param name="scale" value="true"/> + </conditional> + <output name="alignment"> + <assert_contents> + <has_size value="3435977" delta="5000"/> + </assert_contents> + </output> + <output name="fusion_junction_bw" value="test_02.bigwig" ftype="bigwig"/> + </test> + <test expect_num_outputs="1"> + <!--Test 03: Module parse--> + <conditional name="mode"> + <param name="selector" value="parse"/> + <conditional name="aligner"> + <param name="selector" value="MapSplice"/> + <param name="fusion_file" value="mapsplice_chimeric.junction"/> + </conditional> + </conditional> + <output name="parse" value="test_03.bed" ftype="bed"/> + </test> + <test expect_num_outputs="1"> + <!--Test 04: Module parse STAR--> + <conditional name="mode"> + <param name="selector" value="parse"/> + <conditional name="aligner"> + <param name="selector" value="STAR"/> + <param name="fusion_file" value="STAR_chimeric.junction"/> + <param name="f" value="true"/> + </conditional> + </conditional> + <output name="parse" value="test_04.bed" ftype="bed"/> + </test> + <test expect_num_outputs="1"> + <!--Test 05: Module annotate--> + <conditional name="mode"> + <param name="selector" value="annotate"/> + <param name="ref" value="annotation_02.txt"/> + <param name="genome" value="reference_02.fa"/> + <param name="bed" value="test_04.bed"/> + </conditional> + <output name="annotate" value="test_05.tabular" ftype="tabular"/> + </test> + <test expect_num_outputs="2"> + <!--Test 06: Module annotate--> + <conditional name="mode"> + <param name="selector" value="annotate"/> + <param name="ref" value="annotation_02.txt"/> + <param name="genome" value="reference_02.fa"/> + <param name="bed" value="test_04.bed"/> + <param name="no_fix" value="true"/> + <param name="low_confidence" value="true"/> + </conditional> + <output name="annotate" value="test_06.tabular" ftype="tabular"/> + </test> + <test expect_num_outputs="4"> + <!--Test 07: Module de novo--> + <conditional name="mode"> + <param name="selector" value="denovo"/> + <param name="ref" value="annotation_02.txt"/> + <param name="bed" value="test_04.bed"/> + <param name="genome" value="reference_02.fa"/> + <param name="assemble_file" value="assemble.tgz"/> + </conditional> + <output name="denovo_combined" value="test_07_combined.txt" ftype="tabular"/> + <output name="denovo_circularRNA" value="test_07_full.txt" ftype="tabular"/> + <output name="denovo_annotated" value="test_07_annotated.txt" ftype="tabular"/> + <output name="denovo_novel" value="test_07_novel.txt" ftype="tabular"/> + </test> + <test expect_num_outputs="6"> + <!--Test 08: Module de novo additional options--> + <conditional name="mode"> + <param name="selector" value="denovo"/> + <param name="ref" value="annotation_02.txt"/> + <param name="bed" value="test_04.bed"/> + <param name="genome" value="reference_02.fa"/> + <param name="assemble_file" value="assemble.tgz"/> + <param name="abs" value="true"/> + <param name="no_fix" value="true"/> + <param name="rpkm" value="true"/> + </conditional> + <output name="denovo_combined" value="test_08_combined.txt" ftype="tabular"/> + <output name="denovo_circularRNA" value="test_08_full.txt" ftype="tabular"/> + <output name="denovo_annotated" value="test_08_annotated.txt" ftype="tabular"/> + <output name="denovo_novel" value="test_08_novel.txt" ftype="tabular"/> + <output name="denovo_abs5" value="test_08_a5bs.txt" ftype="tabular"/> + <output name="denovo_abs3" value="test_08_a3bs.txt" ftype="tabular"/> + </test> + </tests> + <help><![CDATA[ + +.. class:: infomark + +**Purpose** + +CIRCexplorer2 is a comprehensive and integrative circular RNA analysis toolset. It is the successor +of CIRCexplorer with plenty of new features to facilitate circular RNA identification and characterization. + +------------------- + + .. class:: infomark + +**Features** + + * Precisely annotate circular RNAs (Annotate) + * Support multiple circular RNA aligners (TopHat2/TopHat-Fusion, STAR, MapSplice, BWA and segemehl) (Align and Parse) + * De novo assemble novel circular RNA transcripts (Assemble) + * Characterize various of alternative (back-)splicing events of circular RNAs (Denovo) + * Fast identify circuar RNAs with STAR or BWA (Parse) + * Support both single-read and paired-end sequencing. + +------------------- + +.. class:: infomark + +**Modules** + +CIRCexplorer2 contains 5 modules. Each module functions as an independent component owning its distinctive duty. +Meanwhile, they inteact with each other, and different circular RNA analysis pipelines are derived from different +combinations of several modules. Understanding the detailed mechanism of each module could facilitate your circular +RNA research. + +CIRCexplorer2 documentation is available from `here <http://circexplorer2.readthedocs.org/>`_, including installation instructions and tutorial. + + ]]></help> + <expand macro="citations" /> +</tool>