bowtie2: bowtie2_wrapper.xml comparison

comparison bowtie2_wrapper.xml @ 7:4f92dccc808a draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7

author	devteam
date	Wed, 11 Nov 2015 12:04:23 -0500
parents	e23b0cdeeba6
children	82414e16b6bd

comparison

equal deleted inserted replaced

-:e23b0cdeeba6
+:4f92dccc808a
 <requirements>
 <requirement type="package" version="2.2.4">bowtie2</requirement>
 <requirement type="package" version="0.1.18">samtools</requirement>
 </requirements>
 <command>
 ## prepare bowtie2 index
 #set index_path = ''
 #if str($reference_genome.source) == "history":
 bowtie2-build "$reference_genome.own_file" genome &amp;&amp;
 ln -s "$reference_genome.own_file" genome.fa &amp;&amp;
 #set index_path = 'genome'
 #else:
 #set index_path = $reference_genome.index.fields.path
 #end if
 ## execute bowtie2
 bowtie2
 ## number of threads
 -p \${GALAXY_SLOTS:-4}
 ## index file path
 -x $index_path
 ## Fastq inputs
 #if str( $library.type ) == "single":
 -U "${library.input_1}"
 #if str( $library.unaligned_file ) == "true":
 --un $output_unaligned_reads_l
 #end if
 #if str( $library.unaligned_file ) == "true":
 --un-conc $output_unaligned_reads_l
 #end if
 #end if
 ## Read group information.
 @define_read_group_helpers@
 #if str( $library.type ) == "single":
 #set $rg_auto_name = $read_group_name_default($library.input_1)
 #elif str( $library.type ) == "paired":
 $format_read_group("KS:", $rg_ks, '"', arg='--rg ')
 $format_read_group("PG:", $rg_pg, '"', arg='--rg ')
 $format_read_group("PI:", $rg_pi, '"', arg='--rg ')
 $format_read_group("PU:", $rg_pu, '"', arg='--rg ')
 #end if
 ## Analysis type
 #if ( str( $analysis_type.analysis_type_selector ) == "simple" and str( $analysis_type.presets ) != "no_presets" ):
 $analysis_type.presets
 #elif str( $analysis_type.analysis_type_selector ) == "full":
 #if str( $analysis_type.input_options.input_options_selector ) == "yes":
 --trim3 "${analysis_type.input_options.trim3}"
 ${analysis_type.input_options.qv_encoding}
 ${analysis_type.input_options.solexa_quals}
 ${analysis_type.input_options.int_quals}
 #end if
 #if str( $analysis_type.alignment_options.alignment_options_selector ) == "yes":
 -N "${analysis_type.alignment_options.N}"
 -L "${analysis_type.alignment_options.L}"
 -i "${analysis_type.alignment_options.i}"
 --n-ceil "${analysis_type.alignment_options.n_ceil}"
 #elif str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "local":
 --local
 --score-min "${analysis_type.alignment_options.align_mode.score_min_loc}"
 #end if
 #end if
 #if str( $analysis_type.scoring_options.scoring_options_selector ) == "yes":
 #if ( str( $analysis_type.alignment_options.alignment_options_selector ) == "yes" and str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "local" ):
 --ma "${analysis_type.scoring_options.ma}"
 #end if
 --mp "${analysis_type.scoring_options.mp}"
 --np "${analysis_type.scoring_options.np}"
 --rdg "${analysis_type.scoring_options.rdg_read_open},${analysis_type.scoring_options.rdg_read_extend}"
 --rfg "${analysis_type.scoring_options.rfg_ref_open},${analysis_type.scoring_options.rfg_ref_extend}"
 #end if
 #if str( $analysis_type.reporting_options.reporting_options_selector ) == "k":
 -k "${analysis_type.reporting_options.k}"
 #elif str( $analysis_type.reporting_options.reporting_options_selector ) == "a":
 -a
 #end if
 #if str( $analysis_type.effort_options.effort_options_selector ) == "yes":
 -D "${analysis_type.effort_options.D}"
 -R "${analysis_type.effort_options.R}"
 #end if
 #if str( $analysis_type.sam_options.sam_options_selector ) == "yes":
 ${analysis_type.sam_options.no_unal}
 ${analysis_type.sam_options.omit_sec_seq}
 #end if
 #if str( $analysis_type.other_options.other_options_selector ) == "yes":
+${analysis_type.other_options.reorder}
 ${analysis_type.other_options.non_deterministic}
 --seed "${analysis_type.other_options.seed}"
 #end if
 #elif str( $analysis_type.analysis_type_selector ) == "cline":
 ${analysis_type.cline}
 #end if
--S "galaxy_bowtie_2_output.sam" &amp;&amp;
+## output file
+#if ( str( $analysis_type.analysis_type_selector ) != "full" or str( $analysis_type.sam_opt ) != "true" ):
-## view/sort and output BAM file
+| samtools view -Su - | samtools sort -o - - &gt; $output
-( samtools view -Su "galaxy_bowtie_2_output.sam" | samtools sort -o - - > $output )
+#else
+&gt; $output_sam
+#end if
 ## rename unaligned sequence files
 #if $library.type == "paired" and $output_unaligned_reads_l and $output_unaligned_reads_r:
 #from os.path import splitext
 #set _unaligned_root, _unaligned_ext = splitext( str( $output_unaligned_reads_l ) )
 &amp;&amp; mv "${ _unaligned_root }.1${_unaligned_ext}" "${ output_unaligned_reads_l }"
 &amp;&amp; mv "${ _unaligned_root }.2${_unaligned_ext}" "${ output_unaligned_reads_r }"
 #end if
 </command>
 <!-- basic error handling -->
 <stdio>
 <exit_code range="1:" level="fatal" description="Tool exception" />
 </stdio>
 <inputs>
 <!-- single/paired -->
 <conditional name="library">
 <param name="type" type="select" label="Is this single or paired library">
 <option value="single">Single-end</option>
 <option value="paired">Paired-end</option>
 <option value="paired_collection">Paired-end Dataset Collection</option>
 </param>
 <when value="single">
-<param name="input_1" format="fastqsanger" type="data" label="FASTQ file" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33"/>
+<param name="input_1" format="fastqsanger" type="data" label="FASTQ file" help="Must be of datatype &quot;fastqsanger&quot;" />
 <param name="unaligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write unaligned reads (in fastq format) to separate file(s)" help="--un/--un-conc; This triggers --un parameter for single reads and --un-conc for paired reads" />
 </when>
 <when value="paired">
-<param name="input_1" format="fastqsanger" type="data" label="FASTQ file" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33" />
+<param name="input_1" format="fastqsanger" type="data" label="FASTQ file #1" help="Must be of datatype &quot;fastqsanger&quot;" />
-<param name="input_2" format="fastqsanger" type="data" label="FASTQ file" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33" />
+<param name="input_2" format="fastqsanger" type="data" label="FASTQ file #2" help="Must be of datatype &quot;fastqsanger&quot;" />
 <param name="unaligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write unaligned reads (in fastq format) to separate file(s)" help="--un/--un-conc; This triggers --un parameter for single reads and --un-conc for paired reads" />
 <conditional name="paired_options">
 <param name="paired_options_selector" type="select" label="Do you want to set paired-end options?" help="See &quot;Alignment Options&quot; section of Help below for information">
 <option value="no" selected="True">No</option>
 <option value="yes">Yes</option>
 <option value="--ff">--ff</option>
 </param>
 <param name="no_mixed" type="boolean" truevalue="--no-mixed" falsevalue="" checked="False" label="Disable no-mixed behavior" help="--no-mixed; By default, when `bowtie2` cannot find a concordant or discordant alignment for a pair, it then tries to find alignments for the individual mates; default=False"/>
 <param name="no_discordant" type="boolean" truevalue="--no-discordant" falsevalue="" checked="False" label="Disable no-discordant behavior" help="--no-discordant; By default, `bowtie2` looks for discordant alignments if it cannot find any concordant alignments. A discordant alignment is an alignment where both mates align uniquely, but that does not satisfy the paired-end constraints (`--fr`/`--rf`/`--ff`, `-I`, `-X`); default=False"/>
 <param name="dovetail" type="boolean" truevalue="--dovetail" falsevalue="" checked="False" label="Allow mate dovetailing" help="--dovetail; If the mates `dovetail`, that is if one mate alignment extends past the beginning of the other such that the wrong mate begins upstream, consider that to be concordant. Default=False"/>
-<param name="no_contain" type="boolean" truevalue="--no-contain" falsevalue="" checked="False" label="Allow one mate alignment to contain another" help="--no-contain; If one mate alignment contains the other, consider that to be non-concordant. Default=False"/>
+<param name="no_contain" type="boolean" truevalue="--no-contain" falsevalue="" checked="False" label="Disallow one mate alignment to contain another" help="--no-contain; If one mate alignment contains the other, consider that to be non-concordant. Default=False"/>
-<param name="no_overlap" type="boolean" truevalue="--no-overlap" falsevalue="" checked="False" label="Allow mate alignments to overlap" help="--no-overlap; If one mate alignment overlaps the other at all, consider that to be non-concordant. Default=False"/>
+<param name="no_overlap" type="boolean" truevalue="--no-overlap" falsevalue="" checked="False" label="Disallow mate alignments to overlap" help="--no-overlap; If one mate alignment overlaps the other at all, consider that to be non-concordant. Default=False"/>
 </when>
 <when value="no">
 <!-- do nothing -->
 </when>
 </conditional>
 </when>
 <when value="paired_collection">
-<param name="input_1" format="fastqsanger" type="data_collection" collection_type="paired" label="FASTQ Paired Dataset" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33" />
+<param name="input_1" format="fastqsanger" type="data_collection" collection_type="paired" label="FASTQ Paired Dataset" help="Must be of datatype &quot;fastqsanger&quot;" />
 <param name="unaligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write unaligned reads (in fastq format) to separate file(s)" help="--un/--un-conc; This triggers --un parameter for single reads and --un-conc for paired reads" />
 <conditional name="paired_options">
 <param name="paired_options_selector" type="select" label="Do you want to set paired-end options?" help="See &quot;Alignment Options&quot; section of Help below for information">
 <option value="no" selected="True">No</option>
 <option value="yes">Yes</option>
 <option value="--ff">--ff</option>
 </param>
 <param name="no_mixed" type="boolean" truevalue="--no-mixed" falsevalue="" checked="False" label="Disable no-mixed behavior" help="--no-mixed; By default, when `bowtie2` cannot find a concordant or discordant alignment for a pair, it then tries to find alignments for the individual mates; default=False"/>
 <param name="no_discordant" type="boolean" truevalue="--no-discordant" falsevalue="" checked="False" label="Disable no-discordant behavior" help="--no-discordant; By default, `bowtie2` looks for discordant alignments if it cannot find any concordant alignments. A discordant alignment is an alignment where both mates align uniquely, but that does not satisfy the paired-end constraints (`--fr`/`--rf`/`--ff`, `-I`, `-X`); default=False"/>
 <param name="dovetail" type="boolean" truevalue="--dovetail" falsevalue="" checked="False" label="Allow mate dovetailing" help="--dovetail; If the mates `dovetail`, that is if one mate alignment extends past the beginning of the other such that the wrong mate begins upstream, consider that to be concordant. Default=False"/>
-<param name="no_contain" type="boolean" truevalue="--no-contain" falsevalue="" checked="False" label="Allow one mate alignment to contain another" help="--no-contain; If one mate alignment contains the other, consider that to be non-concordant. Default=False"/>
+<param name="no_contain" type="boolean" truevalue="--no-contain" falsevalue="" checked="False" label="Disallow one mate alignment to contain another" help="--no-contain; If one mate alignment contains the other, consider that to be non-concordant. Default=False"/>
-<param name="no_overlap" type="boolean" truevalue="--no-overlap" falsevalue="" checked="False" label="Allow mate alignments to overlap" help="--no-overlap; If one mate alignment overlaps the other at all, consider that to be non-concordant. Default=False"/>
+<param name="no_overlap" type="boolean" truevalue="--no-overlap" falsevalue="" checked="False" label="Disallow mate alignments to overlap" help="--no-overlap; If one mate alignment overlaps the other at all, consider that to be non-concordant. Default=False"/>
 </when>
 <when value="no">
 <!-- do nothing -->
 </when>
 </conditional>
 <option value="no" selected="true">No</option>
 </param>
 <when value="yes">
 <param name="N" type="integer" min="0" max="1" value="0" label="Set the number of mismatches to be allowed in a seed alignment during multiseed alignment (see `Multiseed alignment` section of help below)" help="-N; Can be set to 0 or 1. Setting this higher makes alignment slower (often much slower) but increases sensitivity; default=0"/>
 <param name="L" type="integer" min="0" max="32" value="22" label="Sets the length of the seed substrings to align during multiseed alignment (see `Multiseed alignment` section of help below)" help="-L; Smaller values make alignment slower but more sensitive. Default=22"/>
-<param name="i" type="text" value="S,1,1.15" size="10" label="Set a function governing the interval between seed substrings to use during multiseed alignment (see `Multiseed alignment` section of help below). Also see description of this option below in the help section" help="-i; Since it's best to use longer intervals for longer reads, this parameter sets the interval as a function of the read length, rather than a single one-size-fits-all number. For instance, specifying `-i S,1,2.5` sets the interval function `f` to `f(x) = 1 + 2.5 * sqrt(x)`, where x is the read length. If the function returns a result less than 1, it is rounded up to 1. Default=`S,1,1.15`"/>
+<param name="i" type="text" value="S,1,1.15" label="Set a function governing the interval between seed substrings to use during multiseed alignment (see `Multiseed alignment` section of help below). Also see description of this option below in the help section" help="-i; Since it's best to use longer intervals for longer reads, this parameter sets the interval as a function of the read length, rather than a single one-size-fits-all number. For instance, specifying `-i S,1,2.5` sets the interval function `f` to `f(x) = 1 + 2.5 * sqrt(x)`, where x is the read length. If the function returns a result less than 1, it is rounded up to 1. Default=`S,1,1.15`"/>
 <param name="n_ceil" type="text" value="L,0,0.15" label="Set a function governing the maximum number of ambiguous characters (usually `N`s and/or `.`s) allowed in a read as a function of read length" help="--n-ceil; For instance, specifying `L,0,0.15` sets the N-ceiling function `f` to `f(x) = 0 + 0.15 * x`, where x is the read length. Reads exceeding this ceiling are filtered out. Default=`L,0,0.15`"/>
 <param name="dpad" type="integer" min="0" value="15" label="Pad dynamic programming problems by that many columns on either side to allow gaps" help="--dpad; default=15"/>
 <param name="gbar" type="integer" min="0" value="4" label="Disallow gaps within that many positions of the beginning or end of the read" help="--gbar; default=4"/>
 <param name="ignore_quals" type="boolean" truevalue="--ignore-quals" falsevalue="" selected="False" label="When calculating a mismatch penalty, always consider the quality value at the mismatched position to be the highest possible, regardless of the actual value" help="--ignore-quals; input is treated as though all quality values are high; default=False"/>
 <param name="nofw" type="boolean" truevalue="--nofw" falsevalue="" selected="False" label="Do not attempt to align unpaired reads to the forward (Watson) reference strand" help="In paired-end mode, `--nofw` and `--norc` pertain to the fragments; i.e. specifying `--nofw` causes `bowtie2` to explore only those paired-end configurations corresponding to fragments from the reverse-complement (Crick) strand. Default=False"/>
 <option value="yes">Yes</option>
 <option value="no" selected="true">No</option>
 </param>
 <when value="yes">
 <param name="ma" type="integer" value="2" label="Set the match bonus" help="--ma;  In `--local` mode match bonus is added to the alignment score for each position where a read character aligns to a reference character and the characters match. Not used in `--end-to-end` mode; Default=2"/>
-<param name="mp" type="text" size="10" value="6,2" label="Set the maximum (`MX`) and minimum (`MN`) mismatch penalties, both integers" help="--mp; A number less than or equal to `MX` and greater than or equal to `MN` is subtracted from the alignment score for each position where a read character aligns to a reference character, the characters do not match, and neither is an `N`.  If `--ignore-quals` is specified, the number subtracted quals `MX`. Otherwise, the number subtracted is `MN + floor( (MX-MN)(MIN(Q, 40.0)/40.0) )` where Q is the Phred quality value; Default=6,2"/>
+<param name="mp" type="text" value="6,2" label="Set the maximum (`MX`) and minimum (`MN`) mismatch penalties, both integers" help="--mp; A number less than or equal to `MX` and greater than or equal to `MN` is subtracted from the alignment score for each position where a read character aligns to a reference character, the characters do not match, and neither is an `N`.  If `--ignore-quals` is specified, the number subtracted quals `MX`. Otherwise, the number subtracted is `MN + floor( (MX-MN)(MIN(Q, 40.0)/40.0) )` where Q is the Phred quality value; Default=6,2"/>
 <param name="np" type="integer" value="1" label="Sets penalty for positions where the read, reference, or both, contain an ambiguous character such as `N`" help="--np; Default=1"/>
 <param name="rdg_read_open" type="integer" value="5" label="Set the read gap opening penalty" help="--rdg; this is the first component of --rdg flag - opening penalty; Default=5"/>
 <param name="rdg_read_extend" type="integer" value="3" label="Set the read gap extension penalty" help="--rdg; this is the second component of --rdg flag - extension penalty; Default=3"/>
 <param name="rfg_ref_open" type="integer" value="5" label="Set the reference gap opening penalty" help="--rfg; this is the first component of --rfg flag - opening penalty; Default=5"/>
 <param name="rfg_ref_extend" type="integer" value="3" label="Set the reference gap extension penalty" help="--rfg; this is the second component of --rfg flag - extension penalty; Default=3"/>
 <param name="other_options_selector" type="select" label="Do you want to tweak Other Options?" help="See &quot;Other Options&quot; section of Help below for information">
 <option value="yes">Yes</option>
 <option value="no" selected="true">No</option>
 </param>
 <when value="yes">
+<param name="reorder" type="boolean" truevalue="--reorder" falsevalue="" label="Guarantee that output SAM records are printed in an order corresponding to the order of the reads in the original input file" help="--reorder; Default=False"/>
 <param name="seed" type="integer" value="0" min="0" label="Use this number as the seed for pseudo-random number generator" help="--seed; Default=0"/>
 <param name="non_deterministic" type="boolean" truevalue="--non-deterministic" falsevalue="" label="Re-initialize the pseudo-random generator for each read using the current time" help="--non-deterministic; see Help below for explanation of this option; default=False"/>
 </when>
 <when value="no">
 <!-- do nothing -->
 </when>
 </conditional>
+<param name="sam_opt" type="boolean" truevalue="true" falsevalue="false" label="Would you like the output to be a SAM file" help="By default, the output from this Bowtie2 wrapper is a sorted BAM file."/>
 </when>
 </conditional>
 </inputs>
 <!-- define outputs -->
 <outputs>
 <data format="fastqsanger" name="output_unaligned_reads_l" label="${tool.name} on ${on_string}: unaligned reads (L)" >
 <filter>library['unaligned_file'] is True</filter>
 <actions>
-<action type="format">
+<conditional name="library.type">
-<option type="from_param" name="library.input_1" param_attribute="ext" />
+<when value="single">
-</action>
+<action type="format">
+<option type="from_param" name="library.input_1" param_attribute="ext" />
+</action>
+</when>
+<when value="paired">
+<action type="format">
+<option type="from_param" name="library.input_1" param_attribute="ext" />
+</action>
+</when>
+<when value="paired_collection">
+<action type="format">
+<option type="from_param" name="library.input_1" param_attribute="forward.ext" />
+</action>
+</when>
+</conditional>
 </actions>
 </data>
 <data format="fastqsanger" name="output_unaligned_reads_r" label="${tool.name} on ${on_string}: unaligned reads (R)">
 <filter>( library['type'] == "paired" or library['type'] == "paired_collection" ) and library['unaligned_file'] is True</filter>
 <actions>
-<action type="format">
+<conditional name="library.type">
-<option type="from_param" name="library.input_1" param_attribute="ext" />
+<when value="paired">
-</action>
+<action type="format">
+<option type="from_param" name="library.input_2" param_attribute="ext" />
+</action>
+</when>
+<when value="paired_collection">
+<action type="format">
+<option type="from_param" name="library.input_1" param_attribute="reverse.ext" />
+</action>
+</when>
+</conditional>
 </actions>
 </data>
 <data format="bam" name="output" label="${tool.name} on ${on_string}: aligned reads (sorted BAM)">
+<filter>analysis_type['analysis_type_selector'] == "simple" or analysis_type['sam_opt'] is False</filter>
+<actions>
+<conditional name="reference_genome.source">
+<when value="indexed">
+<action type="metadata" name="dbkey">
+<option type="from_data_table" name="bowtie2_indexes" column="1" offset="0">
+<filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
+<filter type="param_value" ref="reference_genome.index" column="0"/>
+</option>
+</action>
+</when>
+<when value="history">
+<action type="metadata" name="dbkey">
+<option type="from_param" name="reference_genome.own_file" param_attribute="dbkey" />
+</action>
+</when>
+</conditional>
+</actions>
+</data>
+<data format="sam" name="output_sam" label="${tool.name} on ${on_string}: aligned reads (SAM)">
+<filter>analysis_type['analysis_type_selector'] == "full" and analysis_type['sam_opt'] is True</filter>
 <actions>
 <conditional name="reference_genome.source">
 <when value="indexed">
 <action type="metadata" name="dbkey">
 <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0">

Mercurial > repos > devteam > bowtie2

comparison bowtie2_wrapper.xml @ 7:4f92dccc808a draft