Mercurial > repos > thanhlv > biotradis
changeset 0:afe9a515d145 draft
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
| author | thanhlv |
|---|---|
| date | Thu, 25 Jul 2019 06:03:12 -0400 |
| parents | |
| children | eb1e9759c24e |
| files | biotradis_add_tags.xml biotradis_bacteria_tradis.xml biotradis_check_tags.xml biotradis_filter_tags.xml biotradis_plot.xml biotradis_remove_tags.xml macros.xml |
| diffstat | 7 files changed, 280 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/biotradis_add_tags.xml Thu Jul 25 06:03:12 2019 -0400 @@ -0,0 +1,34 @@ +<tool id="add_tradis_tags" name="add tradis tags" version="@VERSION@"> + <description>Generates a BAM file with tags added to read strings.</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ + + add_tradis_tags -b $input_bam -o added -v > $log + + ]]></command> + <inputs> + <param name="input_bam" type="data" format="bam" label="BAM file" help="" /> + </inputs> + + <outputs> + <data name="log" format="txt" label="${tool.name} on ${on_string} Log" /> + <data name="output_bam" format="bam" label="${tool.name} on ${on_string}" from_work_dir="added.tr.bam" /> + </outputs> + + <tests> + </tests> + <help><![CDATA[ + Adds transposon sequence and quality tags to the read strings and + outputs a BAM. + + Usage: add_tags -b file.bam [options] + + Options: + -b : bam file with tradis tags + -v : verbose debugging output + ]]></help> + +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/biotradis_bacteria_tradis.xml Thu Jul 25 06:03:12 2019 -0400 @@ -0,0 +1,93 @@ +<tool id="add_tradis_tags" name="add tradis tags" version="@VERSION@"> + <description>Generates a BAM file with tags added to read strings.</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ + #import re + + ## Creates symlinks for each input file based on the Galaxy 'element_identifier' + ## Used so that a human-readable name appears in the output table (instead of 'dataset_xyz.dat') + #set $named_input_files = '' + #for $input_file in $input_files + ## Add single quotes around each input file identifier + #set $_input_file = "'{}'".format($input_file.element_identifier) + ln -s '${input_file}' ${_input_file} && + echo ${_input_file} >> fq.list && + #end for + + bacteria_tradis -f fq.list + -t $tag + -r $ref + -td $tag_dir + -mm $mm + -m $m + #if str($smalt_k)!="" + --smalt_k $smalt_k + #end if + #if str($smalt_s)!="" + --smalt_s $smalt_s + #end if + --smalt_y $smalt_y + --smalt_r $smalt_r + -n "\${GALAXY_SLOTS:-2}" + #if $verbose + --verbose + #end if + && tar cvzf insert_site_plot.tar.gz *insert_site_plot.gz + && tar cvzf mapped.tar.gz *mapped.bam* + ]]></command> + <inputs> + <param name="input_files" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" multiple="true" /> + <param name="tag" type="text" label="Tag" help="Tag to search for" /> + <param name="ref" type="data" format="fasta" label="Reference geome" help="Fasta format" /> + <param name="tag_dir" type="select" label="Tag direction" help="3 or 5(optional. default = 3)" > + <option value="3" selected="true">3</option> + <option value="5">5</option> + </param> + <param name="mm" type="integer" value="0" label="Number of mismatches allowed when matching tag" help="(optional. default = 0)" /> + <param name="m" type="integer" value="30" label="Mapping quality cutoff score" help="(optional. default = 30)" /> + <param argument="--smalt_k" type="integer" value="" optional="True" label="Custom k-mer value for SMALT mapping" help="(optional)" /> + <param argument="--smalt_s" type="integer" value="" optional="True" label="Custom step size for SMALT mapping" help="(optional)" /> + <param argument="--smalt_y" type="integer" value="0.96" label="Custom y parameter for SMALT" help="(optional. default = 0.96)" /> + <param argument="--smalt_r" type="integer" value="-1" label="custom r parameter for SMALT" help="(optional. default = -1)" /> + <param argument="--verbose" type="boolean" truevalue="-v" falsevalue="" checked="false" label="verbose debugging output" help="(Default:No)" /> + </inputs> + + <outputs> + <data name="insert_size_plots" format="tar.gz" label="${tool.name} on ${on_string}: Insert size plot" from_work_dir="insert_site_plot.tar.gz"/> + <data name="mapped_bam" format="tar.gz" label="${tool.name} on ${on_string}: Insert size plot" from_work_dir="mapped.tar.gz"/> + <data name="fastq_stats" format="txt" label="${tool.name} on ${on_string}: Fastq Stats" from_work_dir="fastqs.stats"/> + </outputs> + + <help> + <![CDATA[ + Run a TraDIS analysis. This involves: + 1: filtering the data with tags matching that passed via -t option + 2: removing the tags from the sequences + 3: mapping + 4: creating an insertion site plot + 5: creating a stats summary + + Usage: bacteria_tradis [options] + + Options: + -f : text file listing fastq files with tradis tags attached + -t : tag to search for + -r : reference genome in fasta format (.fa) + -td : tag direction - 3 or 5 (optional. default = 3) + -mm : number of mismatches allowed when matching tag (optional. default = 0) + -m : mapping quality cutoff score (optional. default = 30) + --smalt_k : custom k-mer value for SMALT mapping (optional) + --smalt_s : custom step size for SMALT mapping (optional) + --smalt_y : custom y parameter for SMALT (optional. default = 0.96) + --smalt_r : custom r parameter for SMALT (optional. default = -1) + -n : number of threads to use for SMALT and samtools sort (optional. default = 1) + -e : set defaults for essentiality experiment (smalt_r = 0, -m = 0) + -v : verbose debugging output + + Documentation can be found at `site <https://github.com/sanger-pathogens/Bio-Tradis>`_. + ]]></help> + +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/biotradis_check_tags.xml Thu Jul 25 06:03:12 2019 -0400 @@ -0,0 +1,33 @@ +<tool id="check_tradis_tags" name="check tradis tags" version="@VERSION@"> + <description>Check for the existence of tradis tags in a bam</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ + + check_tradis_tags -b $input_bam > $output + + ]]></command> + <inputs> + <param name="input_bam" type="data" format="bam" label="BAM file" help="" /> + </inputs> + + <outputs> + <data name="output" format="tabular" label="${tool.name} on ${on_string}" from_work_dir="$output" /> + </outputs> + + <!-- <tests> + </tests> --> + <help><![CDATA[ + Adds transposon sequence and quality tags to the read strings and + outputs a BAM. + + Usage: add_tags -b file.bam [options] + + Options: + -b : bam file with tradis tags + -v : verbose debugging output + ]]></help> + +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/biotradis_filter_tags.xml Thu Jul 25 06:03:12 2019 -0400 @@ -0,0 +1,36 @@ +<tool id="filter_tradis_tags" name="filter tradis tags" version="@VERSION@"> + <description>Filters a BAM file and outputs reads with tag matching -t option.</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ + + filter_tradis_tags -b $input_bam -t $tag -m $mismatches -o filtered + + ]]></command> + <inputs> + <param name="input_bam" type="data" format="bam" label="BAM file" help="" /> + <param name="tag" type="text" label="Tags to filter" help="" /> + <param name="mismatches" type="integer" value ="0" label="Number of mismatches to allow when matching tag" help="(optional. default = 0)" /> + <param argument="--verbose" type="boolean" truevalue="-v" falsevalue="" checked="false" label="verbose debugging output" help="(Default:No)" /> + </inputs> + + <outputs> + <data name="filtered_tags" format="fastq" label="${tool.name} on ${on_string}" from_work_dir="filtered.tag.fatsq" /> + </outputs> + + <!-- <tests> + </tests> --> + <help><![CDATA[ + Adds transposon sequence and quality tags to the read strings and + outputs a BAM. + + Usage: add_tags -b file.bam [options] + + Options: + -b : bam file with tradis tags + -v : verbose debugging output + ]]></help> + +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/biotradis_plot.xml Thu Jul 25 06:03:12 2019 -0400 @@ -0,0 +1,34 @@ +<tool id="add_tradis_tags" name="add tradis tags" version="@VERSION@"> + <description>Create insertion site plot for Artemis</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ + + tradis_plot -b $input_bam -m $mapping_quality + + ]]></command> + <inputs> + <param name="input_bam" type="data" format="bam" label="BAM file" help="" /> + <param name="mapping_quality" type="integer" value="30" label="mapping quality must be greater than X " help="(optional. default: 30)" /> + </inputs> + + <outputs> + <data name="output_bam" format="bam" label="${tool.name} on ${on_string}" from_work_dir="added.tr.bam" /> + </outputs> + + <tests> + </tests> + <help><![CDATA[ + Adds transposon sequence and quality tags to the read strings and + outputs a BAM. + + Usage: add_tags -b file.bam [options] + + Options: + -b : bam file with tradis tags + -v : verbose debugging output + ]]></help> + +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/biotradis_remove_tags.xml Thu Jul 25 06:03:12 2019 -0400 @@ -0,0 +1,36 @@ +<tool id="remove_tradis_tags" name="remove tradis tags" version="@VERSION@"> + <description>Removes transposon sequence and quality tags from the read strings</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ + + remove_tags -f $input_bam -t $tag -m $mismatches -o removed -v > $log + + ]]></command> + <inputs> + <param name="input_fastq" type="data" format="fastq" label="Fastq file" help="" /> + <param name="tag" type="text" label="Tags to remove" help="" /> + <param name="mismatches" type="integer" value ="0" label="Number of mismatches to allow when matching tag" help="(optional. default = 0)" /> + </inputs> + + <outputs> + <data name="log" format="txt" label="${tool.name} on ${on_string}: Log"/> + <data name="filtered_tags" format="fastqsanger" label="${tool.name} on ${on_string}" from_work_dir="removed.rmtag.fatsq" /> + </outputs> + + <tests> + </tests> + <help><![CDATA[ + Adds transposon sequence and quality tags to the read strings and + outputs a BAM. + + Usage: add_tags -b file.bam [options] + + Options: + -b : bam file with tradis tags + -v : verbose debugging output + ]]></help> + +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Thu Jul 25 06:03:12 2019 -0400 @@ -0,0 +1,14 @@ +<macros> + <token name="@VERSION@">1.4.1.dev</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@VERSION@">biotradis</requirement> + </requirements> + </xml> + + <xml name="citations"> + <citations> + <citation type="doi">10.1093/bioinformatics/btw022</citation> + </citations> + </xml> +</macros> \ No newline at end of file