Mercurial > repos > weilong-guo > bs_seeker2
diff BSseeker2/galaxy/bs_seeker2_wrapper.xml @ 1:8b26adf64adc draft default tip
V2.0.5
| author | weilong-guo |
|---|---|
| date | Tue, 05 Nov 2013 01:55:39 -0500 |
| parents | e6df770c0e58 |
| children |
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--- a/BSseeker2/galaxy/bs_seeker2_wrapper.xml Fri Jul 12 18:47:28 2013 -0400 +++ b/BSseeker2/galaxy/bs_seeker2_wrapper.xml Tue Nov 05 01:55:39 2013 -0500 @@ -1,255 +1,270 @@ -<tool id="bs_seeker_wrapper" name="BS-Seeker2" version="2.0.0"> - <requirements><requirement type='package'>bs_seeker2</requirement></requirements> - <description>Versatile aligner for bisulfite sequencing data</description> - <command interpreter="python"> - bs_seeker2_wrapper.py - ### define exec path - ### --exec-path "/u/home/galaxy/galaxy/GalaxyTools/bin" - ### [Please change the following path to your local directory] - --exec-path "/Users/weilong/Documents/program/BSseeker2" - ### output - --align--output $align_output - --call_methylation--wig $call_methylation_wig - --call_methylation--CGmap $call_methylation_CGmap - --call_methylation--ATCGmap $call_methylation_ATCGmap - --call_methylation--txt - - #if $singlePaired.sPaired == "paired" - --align--input_1 $input1 - --align--input_2 $singlePaired.input2 - #end if - - - ### aligner - --align--aligner ${choosealigner.aligner} - - ### Index from history or built-in - #if $choosealigner.rrbsFragments.refGenomeSource.genomeSource == "history" - --build--file ${choosealigner.rrbsFragments.refGenomeSource.ownFile} - --build--aligner ${choosealigner.aligner} - --align-g ${choosealigner.rrbsFragments.refGenomeSource.ownFile} - --align--db ${choosealigner.rrbsFragments.refGenomeSource.ownFile} - #else if $choosealigner.rrbsFragments.refGenomeSource.genomeSource == "indexed" - --align--db ${choosealigner.rrbsFragments.refGenomeSource.index.fields.path} - --align-g ${choosealigner.rrbsFragments.refGenomeSource.index.fields.path}/${choosealigner.rrbsFragments.refGenomeSource.index.fields.dbkey}.fa - - #end if - - ### RRBS or WGBS - #if $choosealigner.rrbsFragments.Fragmented == "Yes" - #if $choosealigner.rrbsFragments.refGenomeSource.genomeSource == "history" - --build--rrbs - --build--low ${choosealigner.rrbsFragments.lowerBound} - --build--up ${choosealigner.rrbsFragments.upperBound} - #end if - --align--rrbs - --align--low ${choosealigner.rrbsFragments.lowerBound} - --align--up ${choosealigner.rrbsFragments.upperBound} - #end if - - - - ### Inputs - #if $singlePaired.sPaired == "single" - --align-i $input1 - #end if - - ### Library type - --align-t $tag - - ### other general options - #if $sParams.sSettingsType == "preSet" - --align--start_base 1 - --align--end_base 200 - --align--mis 4 - #end if - - ### adapter information - #if $adapterInfo.useAdapter == "Yes" - --align--adapter ${adapterInfo.adapter_file} - #end if - - #if $sParams.sSettingsType == "full" - --align--start_base ${sParams.start_base} - --align--end_base ${sParams.end_base} - --align--mis ${sParams.num_mismatch} - #end if - - </command> - <inputs> - <param format="fastq,fasta,qseq" name="input1" type="data" label="Input your read file" help="reads file in fastq, qseq or fasta format" /> - <conditional name="singlePaired"> - <param name="sPaired" type="select" label="Is this library mate-paired?"> - <option value="single">Single-end</option> - <option value="paired">Paired-end</option> - </param> - <when value="paired"> - <param format="fastq,fasta,qseq" name="input2" type="data" label="Input your read file 2" help="reads in fastq, qseq or fasta format" /> - <param name="min_ins_distance" type="integer" value="-1" label=" Minimum insert size for valid paired-end alignments" /> - <param name="max_ins_distance" type="integer" value="400" label="Maximum insert size for valid paired-end alignments" /> - </when> - </conditional> - <param name="tag" type="select" label="Type of libraries"> - <option value="N">directional libraries</option> - <option value="Y">undirectional libraries</option> - </param> - <conditional name="choosealigner"> - <param name="aligner" type="select" label="Short reads aligner"> - <option value="bowtie">bowtie</option> - <option value="bowtie2">bowtie2</option> - </param> - <when value="bowtie"> - <conditional name="rrbsFragments"> - <param name="Fragmented" type="select" label="RRBS-seq reads" help=""> - <option value="No">No</option> - <option value="Yes">Yes</option> - </param> - <when value="Yes"> - <param name="lowerBound" type="integer" value="40" label="The lower bound for RRBS fragments" help="Default: 40" /> - <param name="upperBound" type="integer" value="500" label="The upper bound for RRBS fragments" help="Default: 500" /> - <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=""> - <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 (RRBS, bowtie)"> - <options from_data_table="bs_seeker2_indexes_RRBS_bowtie"> - <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> - </conditional> - </when> - <when value="No"> - <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=""> - <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 (WGBS, bowtie)"> - <options from_data_table="bs_seeker2_indexes_WGBS_bowtie"> - <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> - </conditional> - </when> - </conditional> - </when> - - <when value="bowtie2"> - <conditional name="rrbsFragments"> - <param name="Fragmented" type="select" label="RRBS-seq reads" help=""> - <option value="No">No</option> - <option value="Yes">Yes</option> - </param> - <when value="Yes"> - <param name="lowerBound" type="integer" value="40" label="The lower bound for RRBS fragments" help="Default: 40" /> - <param name="upperBound" type="integer" value="500" label="The upper bound for RRBS fragments" help="Default: 500" /> - <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=""> - <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 (RRBS, bowtie2)"> - <options from_data_table="bs_seeker2_indexes_RRBS_bowtie2"> - <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> - </conditional> - </when> - <when value="No"> - <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=""> - <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 (WGBS, bowtie2)"> - <options from_data_table="bs_seeker2_indexes_WGBS_bowtie2"> - <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> - </conditional> - </when> - </conditional> - </when> - </conditional> - <conditional name="adapterInfo"> - <param name="useAdapter" type="select" label="adapter sequence"> - <option value="noAdapter">No</option> - <option value="withAdapter">Yes</option> - </param> - <when value="withAdapter"> - <param format="txt" name="adapter_file" type="data" label="Input file of your adaptor sequences" help="Input text file of your adaptor sequences" /> - </when> - </conditional> - - <conditional name="sParams"> - <param name="sSettingsType" type="select" label="BS Seeker2 settings to use" help="You can use the default settings or set customer values for the BS Seeker2 parameters."> - <option value="preSet">User Defaults</option> - <option value="full">Full parameter list</option> - </param> - <when value="preSet" /> - <when value="full"> - <param name="start_base" type="integer" value="1" label="The start base of the read to be mapped" help="" /> - <param name="end_base" type="integer" value="200" label="The end base of the read to be mapped" help="" /> - - <param name="num_mismatch" type="integer" value="4" label="Number of mismatches" help="(INT) Default: 4" /> - </when> - </conditional> - -</inputs> - - <outputs> - <data format="bam" name="align_output" label="BAM Alignments"> </data> - <data format="wig" name="call_methylation_wig" label="Methylation Levels"> </data> - <data format="tabular" name="call_methylation_CGmap" label="CGmap file"> </data> - <data format="tabular" name="call_methylation_ATCGmap" label="ATCGmap file"> </data> - - </outputs> - <help> -**What it does** - -BS-Seeker2 is a seamlessly pipeline for mapping bisulfite sequencing data and generating detailed DNA methylome. BS-Seeker2 improves mappability by using local alignment, and is tailored for RRBS library by building special index, with higher efficiency and accuracy. This is the Galaxy version of BS-Seeker2. - ------- - -**Resources** - -The homepage for BS-Seeker2 is http://pellegrini.mcdb.ucla.edu/BS_Seeker2/. - -For more information of BS-Seeker2, please refer to https://github.com/BSSeeker/BSseeker2. - ------- - -**Example** - -- Adapter file:: - - AGATCGGAAGAGCACACGTC - - - </help> -</tool> +<tool id="bs_seeker_wrapper" name="BS-Seeker2" version="2.0.0"> + <requirements><requirement type='package'>bs_seeker2</requirement></requirements> + <description>Versatile aligner for bisulfite sequencing data</description> + <command interpreter="python"> + bs_seeker2_wrapper.py + ### define exec path + ### --exec-path "/u/home/galaxy/galaxy/GalaxyTools/bin" + ### [Please change the following path to your local directory] + --exec-path "/Users/weilong/Documents/program/BSseeker2" + ### output + --align--output $align_output + --call_methylation--wig $call_methylation_wig + --call_methylation--CGmap $call_methylation_CGmap + --call_methylation--ATCGmap $call_methylation_ATCGmap + --call_methylation--txt + + #if $singlePaired.sPaired == "paired" + --align--input_1 $input1 + --align--input_2 $singlePaired.input2 + #end if + + + ### aligner + --align--aligner ${choosealigner.aligner} + #if $choosealigner.aligner == "bowtie2" + #if $choosealigner.mode_type == "local" + --align--bt2--local + #else + --align--bt2--end-to-end + #end if + #end if + + ### Index from history or built-in + #if $choosealigner.rrbsFragments.refGenomeSource.genomeSource == "history" + --build--file ${choosealigner.rrbsFragments.refGenomeSource.ownFile} + --build--aligner ${choosealigner.aligner} + --align-g ${choosealigner.rrbsFragments.refGenomeSource.ownFile} + --align--db ${choosealigner.rrbsFragments.refGenomeSource.ownFile} + #else if $choosealigner.rrbsFragments.refGenomeSource.genomeSource == "indexed" + --align--db ${choosealigner.rrbsFragments.refGenomeSource.index.fields.path} + --align-g ${choosealigner.rrbsFragments.refGenomeSource.index.fields.path}/${choosealigner.rrbsFragments.refGenomeSource.index.fields.dbkey}.fa + + #end if + + ### RRBS or WGBS + #if $choosealigner.rrbsFragments.Fragmented == "Yes" + #if $choosealigner.rrbsFragments.refGenomeSource.genomeSource == "history" + --build--rrbs + --build--low ${choosealigner.rrbsFragments.lowerBound} + --build--up ${choosealigner.rrbsFragments.upperBound} + #end if + --align--rrbs + --align--low ${choosealigner.rrbsFragments.lowerBound} + --align--up ${choosealigner.rrbsFragments.upperBound} + #end if + + + + ### Inputs + #if $singlePaired.sPaired == "single" + --align-i $input1 + #end if + + ### Library type + --align-t $tag + + ### other general options + #if $sParams.sSettingsType == "preSet" + --align--start_base 1 + --align--end_base 200 + --align--mis 4 + #end if + + ### adapter information + #if $adapterInfo.useAdapter == "Yes" + --align--adapter ${adapterInfo.adapter_file} + #end if + + #if $sParams.sSettingsType == "full" + --align--start_base ${sParams.start_base} + --align--end_base ${sParams.end_base} + --align--mis ${sParams.num_mismatch} + #end if + + </command> + <inputs> + <param format="fastq,fasta,qseq" name="input1" type="data" label="Input your read file" help="reads file in fastq, qseq or fasta format" /> + <conditional name="singlePaired"> + <param name="sPaired" type="select" label="Is this library mate-paired?"> + <option value="single">Single-end</option> + <option value="paired">Paired-end</option> + </param> + <when value="paired"> + <param format="fastq,fasta,qseq" name="input2" type="data" label="Input your read file 2" help="reads in fastq, qseq or fasta format" /> + <param name="min_ins_distance" type="integer" value="-1" label=" Minimum insert size for valid paired-end alignments" /> + <param name="max_ins_distance" type="integer" value="400" label="Maximum insert size for valid paired-end alignments" /> + </when> + </conditional> + <param name="tag" type="select" label="Type of libraries"> + <option value="N">directional libraries</option> + <option value="Y">undirectional libraries</option> + </param> + <conditional name="choosealigner"> + <param name="aligner" type="select" label="Short reads aligner"> + <option value="bowtie">bowtie</option> + <option value="bowtie2">bowtie2</option> + </param> + <when value="bowtie"> + <conditional name="rrbsFragments"> + <param name="Fragmented" type="select" label="RRBS-seq reads" help=""> + <option value="No">No</option> + <option value="Yes">Yes</option> + </param> + <when value="Yes"> + <param name="lowerBound" type="integer" value="40" label="The lower bound for RRBS fragments" help="Default: 40" /> + <param name="upperBound" type="integer" value="500" label="The upper bound for RRBS fragments" help="Default: 500" /> + <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=""> + <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 (RRBS, bowtie)"> + <options from_data_table="bs_seeker2_indexes_RRBS_bowtie"> + <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> + </conditional> + </when> + <when value="No"> + <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=""> + <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 (WGBS, bowtie)"> + <options from_data_table="bs_seeker2_indexes_WGBS_bowtie"> + <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> + </conditional> + </when> + </conditional> + </when> + + <when value="bowtie2"> + <conditional name="rrbsFragments"> + <param name="Fragmented" type="select" label="RRBS-seq reads" help=""> + <option value="No">No</option> + <option value="Yes">Yes</option> + </param> + <when value="Yes"> + <param name="lowerBound" type="integer" value="40" label="The lower bound for RRBS fragments" help="Default: 40" /> + <param name="upperBound" type="integer" value="500" label="The upper bound for RRBS fragments" help="Default: 500" /> + <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=""> + <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 (RRBS, bowtie2)"> + <options from_data_table="bs_seeker2_indexes_RRBS_bowtie2"> + <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> + </conditional> + </when> + <when value="No"> + <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=""> + <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 (WGBS, bowtie2)"> + <options from_data_table="bs_seeker2_indexes_WGBS_bowtie2"> + <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> + </conditional> + </when> + </conditional> + + + <conditional name="mode_type"> + <param name="mode" type="select" label="Select the mode of Bowtie2"> + <option value="local" selected="true"> local alignment </option> + <option value="end_to_end" > end-to-end alignment </option> + </param> + </conditional> + </when> + </conditional> + <conditional name="adapterInfo"> + <param name="useAdapter" type="select" label="adapter sequence"> + <option value="noAdapter">No</option> + <option value="withAdapter">Yes</option> + </param> + <when value="withAdapter"> + <param format="txt" name="adapter_file" type="data" label="Input file of your adaptor sequences" help="Input text file of your adaptor sequences" /> + </when> + </conditional> + + <conditional name="sParams"> + <param name="sSettingsType" type="select" label="BS Seeker2 settings to use" help="You can use the default settings or set customer values for the BS Seeker2 parameters."> + <option value="preSet">User Defaults</option> + <option value="full">Full parameter list</option> + </param> + <when value="preSet" /> + <when value="full"> + <param name="start_base" type="integer" value="1" label="The start base of the read to be mapped" help="" /> + <param name="end_base" type="integer" value="200" label="The end base of the read to be mapped" help="" /> + + <param name="num_mismatch" type="integer" value="4" label="Number of mismatches" help="(INT) Default: 4" /> + </when> + </conditional> + +</inputs> + + <outputs> + <data format="bam" name="align_output" label="BAM Alignments"> </data> + <data format="wig" name="call_methylation_wig" label="Methylation Levels"> </data> + <data format="tabular" name="call_methylation_CGmap" label="CGmap file"> </data> + <data format="tabular" name="call_methylation_ATCGmap" label="ATCGmap file"> </data> + + </outputs> + <help> +**What it does** + +BS-Seeker2 is a seamlessly pipeline for mapping bisulfite sequencing data and generating detailed DNA methylome. BS-Seeker2 improves mappability by using local alignment, and is tailored for RRBS library by building special index, with higher efficiency and accuracy. This is the Galaxy version of BS-Seeker2. + +------ + +**Resources** + +The homepage for BS-Seeker2 is http://pellegrini.mcdb.ucla.edu/BS_Seeker2/. + +For more information of BS-Seeker2, please refer to https://github.com/BSSeeker/BSseeker2. + +------ + +**Example** + +- Adapter file:: + + AGATCGGAAGAGCACACGTC + + + </help> +</tool>