Mercurial > repos > iuc > mixcr_analyze
diff mixcr_analyze.xml @ 0:d38cfb922f95 draft default tip
"planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
| author | iuc |
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| date | Thu, 10 Oct 2019 18:03:22 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mixcr_analyze.xml Thu Oct 10 18:03:22 2019 -0400 @@ -0,0 +1,271 @@ +<tool id="mixcr_analyze" name="MiXCR Analyze" version="@VERSION@.0"> + <description>immuno clonotyes from sequence data</description> + <macros> + <import>mixcr_macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ + #import os.path + #import re + #def clean(name) + #set $base_name = $os.path.basename($name) + #set $name_clean = re.sub('[^\w\-_\.]', '_', $base_name) + #return $name_clean + #end def + #if $imgt.library_selector == 'history': + #set $libname = $re.sub('.gz$','',$clean($imgt.library.name)) + ln -s -f '$imgt.library' $libname && + #end if + #if str( $fastq_input.fastq_input_selector ) == "paired": + #set $fq1 = $clean($fastq_input.fastq_input1.name) + ln -s -f '$fastq_input.fastq_input1' $fq1 && + #set $fq2 = $clean($fastq_input.fastq_input2.name) + ln -s -f '$fastq_input.fastq_input2' $fq2 && + #else: + #set $fq1 = $clean($fastq_input.fastq_input1.name) + ln -s -f '$fastq_input.fastq_input1' $fq1 && + #end if + mixcr analyze $analyze.pipeline --starting-material $starting_material + #if $analyze.pipeline == 'amplicon': + --5-end $analyze.primers5end + --3-end $analyze.primers3end + --adapters $analyze.adapters + #end if + #if $imgt.library_selector == 'history': + --align "--library $libname" + #set $taxonId = str($imgt.species).split(':')[0] + --species $taxonId + ## #elif $imgt.library_selector == 'cached': + #else + --species $imgt.species + #end if + $contig_assembly $impute_germline_on_export $only_productive + --receptor-type $receptor_type + #if str( $fastq_input.fastq_input_selector ) == "paired": + $fq1 $fq2 + #else: + $fq1 + #end if + mixcr_analysis + ]]></command> + <inputs> + <conditional name="analyze"> + <param name="pipeline" type="select" label="amplicon or shotgun data" help=""> + <option value="amplicon">amplicon: enriched targeted TCR/IG libraries (5’RACE, Amplicon, Multiplex, etc)</option> + <option value="shotgun">shotgun: non-enriched RNA-seq or non-targeted genomic data</option> + </param> + <when value="amplicon"> + <param name="primers5end" type="select" label="5’-end of the library."> + <help> + There are two possible values: + no-v-primers — no V gene primers (e.g. 5’RACE with template switch oligo or a like), + v-primers — V gene single primer / multiple. + </help> + <option value="no-v-primers">no-v-primers</option> + <option value="v-primers">v-primers</option> + </param> + <param name="primers3end" type="select" label="3’-end of the library."> + <help> + There are three possible values: + j-primers — J gene single primer / multiplex, + j-c-intron-primers — J-C intron single primer / multiplex, + c-primers — C gene single primer / multiplex (e.g. IGHC primers specific to different immunoglobulin isotypes). + </help> + <option value="j-primers">j-primers</option> + <option value="j-c-intron-primers">j-c-intron-primers</option> + <option value="c-primers">c-primers</option> + </param> + <param name="adapters" type="select" label="Presence of PCR primers and/or adapter sequences"> + <help> + If sequences of primers used for PCR or adapters are present in sequencing data, + it may influence the accuracy of V, J and C gene segments identification and CDR3 mapping. + </help> + <option value="adapters-present">adapters-present</option> + <option value="no-adapters">no-adapters</option> + </param> + </when> + <when value="shotgun"/> + </conditional> + <param name="starting_material" type="select" label="Type of starting material: RNA or DNA" help=""> + <option value="rna">RNA</option> + <option value="dna">DNA</option> + </param> + <conditional name="fastq_input"> + <param name="fastq_input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single end data"> + <option value="single">single-end fastq</option> + <option value="paired">paired-end fastq</option> + </param> + <when value="paired"> + <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Select first set of reads" help="Specify dataset with forward reads"/> + <param name="fastq_input2" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Select second set of reads" help="Specify dataset with reverse reads"/> + </when> + <when value="single"> + <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" label="Select sequence dataset" help="Specify dataset with single reads"/> + </when> + </conditional> + <conditional name="imgt"> + <param name="library_selector" type="select" label="Library selector" help="Select between paired and single end data"> + <option value="builtin">MiXCR builtin library</option> + <!-- <option value="cached">repseqio IMGT library</option> --> + <option value="history">history repseqio IMGT library</option> + </param> + <when value="builtin"> + <param name="species" type="text" label="Species"> + <option value="9606">HomoSapiens</option> + <option value="MusMusculus">MusMusculus</option> + <option value="rat">rat</option> + </param> + </when> + <!-- + <when value="cached"> + <param name="library" type="select" label="repseqio IMGT library"> + <options from_data_table="imgt_library"> + <column name="name" index="1"/> + <column name="value" index="2"/> + </options> + </param> + <param name="species" type="select" label="Species"> + <options from_data_table="imgt_library"> + <column name="name" index="3"/> + <column name="value" index="3"/> + <filter type="param_value" ref="library" column="2" /> + <filter type="multiple_splitter" column="3" separator=","/> + </options> + </param> + </when> + --> + <when value="history"> + <param name="library" type="data" format="imgt.json" label="repseqio IMGT library"> + <help><![CDATA[ +Data coming from IMGT server may be used for academic research only, +provided that it is referred to IMGT®, and cited as:MiXCR is a universal framework that processes big immunome data from raw sequences to quantitated clonotypes. MiXCR efficiently handles paired- and single-end reads, considers sequence quality, corrects PCR errors and identifies germline hypermutations. The software supports both partial- and full-length profiling and employs all available RNA or DNA information, including sequences upstream of V and downstream of J gene segments. + +MiXCR is free for academic and non-profit use (see License). +"IMGT®, the international ImMunoGeneTics information system® http://www.imgt.org (founder and director: Marie-Paule Lefranc, Montpellier, France)." + ]]></help> + </param> + <param name="species" type="select" label="Species"> + <options> + <filter type="data_meta" ref="library" key="taxon_names" /> + </options> + </param> + </when> + </conditional> + <param name="contig_assembly" type="boolean" truevalue="--contig-assembly" falsevalue="" checked="false" label="Assemble full receptor sequences." help="This option may slow down the computation."/> + <param name="impute_germline_on_export" type="boolean" truevalue="--impute-germline-on-export" falsevalue="" checked="false" label="Use germline segments (printed with lowercase letters) for uncovered gene features"/> + <param name="only_productive" type="boolean" truevalue="--only-productive" falsevalue="" checked="false" label="Filter out-of-frame and stop-codons in export"/> + <param name="receptor_type" type="select" label="Dedicated receptor type for analysis"> + <option value="xcr" selected="true">xcr (all T- and B-cell receptor chains are analyzed)</option> + <option value="tcr">tcr</option> + <option value="bcr">bcr</option> + <option value="tra">tra</option> + <option value="trb">trb</option> + <option value="trg">trg</option> + <option value="trd">trd</option> + <option value="igh">igh</option> + <option value="igk">igk</option> + <option value="igl">igl</option> + </param> + </inputs> + <outputs> + <data name="report" format="txt" label="${tool.name} on ${on_string}: report" from_work_dir="mixcr_analysis.report"/> + <data name="clonotypes" format="tabular" label="${tool.name} on ${on_string}: clonotypes.ALL" from_work_dir="mixcr_analysis.clonotypes.ALL.txt"> + <actions> + <action name="comment_lines" type="metadata" default="1" /> + <action name="column_names" type="metadata" default="cloneId,cloneCount,cloneFraction,targetSequences,targetQualities,allVHitsWithScore,allDHitsWithScore,allJHitsWithScore,allCHitsWithScore,allVAlignments,allDAlignments,allJAlignments,allCAlignments,nSeqFR1,minQualFR1,nSeqCDR1,minQualCDR1,nSeqFR2,minQualFR2,nSeqCDR2,minQualCDR2,nSeqFR3,minQualFR3,nSeqCDR3,minQualCDR3,nSeqFR4,minQualFR4,aaSeqFR1,aaSeqCDR1,aaSeqFR2,aaSeqCDR2,aaSeqFR3,aaSeqCDR3,aaSeqFR4,refPoints" /> + </actions> + </data> + </outputs> + <tests> + <test> + <conditional name="analyze"> + <param name="pipeline" value="shotgun"/> + </conditional> + <param name="starting_material" value="rna"/> + <conditional name="fastq_input"> + <param name="fastq_input_selector" value="paired"/> + <param name="fastq_input1" value="sample_IGH_R1.fastq" ftype="fastqsanger"/> + <param name="fastq_input2" value="sample_IGH_R2.fastq" ftype="fastqsanger"/> + </conditional> + <conditional name="imgt"> + <param name="library_selector" value="builtin"/> + <param name="species" value="9606"/> + </conditional> + <param name="contig_assembly" value="True"/> + <param name="impute_germline_on_export" value="True"/> + <param name="only_productive" value="False"/> + <param name="receptor_type" value="xcr"/> + <output name="report"> + <assert_contents> + <has_text text="Final clonotype count" /> + </assert_contents> + </output> + <output name="clonotypes"> + <assert_contents> + <has_text text="CARDDGGGKGDYGRLW" /> + </assert_contents> + </output> + </test> + <test> + <conditional name="analyze"> + <param name="pipeline" value="amplicon"/> + <param name="primers5end" value="v-primers"/> + <param name="primers3end" value="j-primers"/> + <param name="adapters" value="no-adapters"/> + </conditional> + <param name="starting_material" value="rna"/> + <conditional name="fastq_input"> + <param name="fastq_input_selector" value="paired"/> + <param name="fastq_input1" value="sample_IGH_R1.fastq" ftype="fastqsanger"/> + <param name="fastq_input2" value="sample_IGH_R2.fastq" ftype="fastqsanger"/> + </conditional> + <conditional name="imgt"> + <param name="library_selector" value="builtin"/> + <param name="species" value="9606"/> + </conditional> + <param name="contig_assembly" value="True"/> + <param name="impute_germline_on_export" value="True"/> + <param name="only_productive" value="False"/> + <param name="receptor_type" value="xcr"/> + <output name="report"> + <assert_contents> + <has_text text="Final clonotype count" /> + </assert_contents> + </output> + <output name="clonotypes"> + <assert_contents> + <has_text text="CARDDGGGKGDYGRLW" /> + </assert_contents> + </output> + </test> + + </tests> + <help><![CDATA[ +**MiXCR** **a universal tool for fast and accurate analysis of T- and B- cell receptor repertoire sequencing data** + +MiXCR_ is a universal framework that processes big immunome data from raw sequences to quantitated clonotypes. MiXCR_ efficiently handles paired- and single-end reads, considers sequence quality, corrects PCR errors and identifies germline hypermutations. The software supports both partial- and full-length profiling and employs all available RNA or DNA information, including sequences upstream of V and downstream of J gene segments. + +**MiXCR is free for academic and non-profit use** (see License_). + +This tool runs the MiXCR_ analyze_ pipeline. +Generally, there two distinct types of library preparation which correspond to the two analyze pipelines: + + - analyze_ amplicon_ for analysis of targeted TCR/IG library amplification (5’RACE, Amplicon, Multiplex, etc). + - analyze_ shotgun_ for analysis of random fragments (RNA-Seq, Exome-Seq, etc). + + +MiXCR_ has builtin libraries for human, mouse and rat. Additional compiled IMGT_ libraries can be imported into your Galaxy history as datatype: *imgt.json* from: https://github.com/repseqio/library-imgt/releases + +NOTE: The imgt.201822-5.sv4.json.gz release has the rattus genus taxonId:10114 for rat, whereas the mixcr builtin library has the rattus norvegicus species taxId:10116 for rat. If you encounter imgt library loading errors from mixcr, you may have to substitute 10116 for 10114 in the imgt.201822-5.sv4.json.gz file. + +**Data coming from IMGT server may be used for academic research only**, provided that it is referred to IMGT®, and cited as "IMGT®, the international ImMunoGeneTics information system® http://www.imgt.org (founder and director: Marie-Paule Lefranc, Montpellier, France)." + +.. _MiXCR: https://mixcr.readthedocs.io/en/latest/index.html +.. _analyze: https://mixcr.readthedocs.io/en/latest/analyze.html +.. _amplicon: https://mixcr.readthedocs.io/en/latest/analyze.html#analysis-of-targeted-tcr-ig-libraries +.. _shotgun: https://mixcr.readthedocs.io/en/latest/analyze.html#analysis-of-non-enriched-or-random-fragments +.. _License: https://mixcr.readthedocs.io/en/latest/license.html#license +.. _IMGT: https://github.com/repseqio/library-imgt/releases + ]]></help> + <expand macro="citations" /> +</tool>