Mercurial > repos > devteam > picard
diff picard_FastqToSam.xml @ 33:3f254c5ced1d draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
| author | iuc |
|---|---|
| date | Sun, 03 Mar 2024 16:06:11 +0000 |
| parents | f9242e01365a |
| children |
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--- a/picard_FastqToSam.xml Mon Sep 25 08:32:17 2023 +0000 +++ b/picard_FastqToSam.xml Sun Mar 03 16:06:11 2024 +0000 @@ -1,13 +1,13 @@ -<tool name="FastqToSam" id="picard_FastqToSam" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="20.01"> +<tool name="FastqToSam" id="picard_FastqToSam" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="@PROFILE@"> <description>convert Fastq data into unaligned BAM</description> <macros> <import>picard_macros.xml</import> - <token name="@WRAPPER_VERSION@">2</token> + <token name="@WRAPPER_VERSION@">0</token> </macros> <xrefs> <xref type="bio.tools">picard_fastqtosam</xref> </xrefs> - <expand macro="requirements" /> + <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ @java_options@ #if str( $input_type.input_type_selector ) == "se": @@ -24,145 +24,138 @@ #if $fwd.ext.endswith(".gz") gunzip -c '$fwd' > fwd.fastq && #else - ln -s '$fwd' fwd.fastq && + ln -sf '$fwd' fwd.fastq && #end if #if rev #if rev.ext.endswith(".gz") gunzip -c '$rev' > rev.fastq && #else - ln -s '$rev' rev.fastq && + ln -sf '$rev' rev.fastq && #end if #end if - picard - FastqToSam + picard FastqToSam - FASTQ=fwd.fastq + --FASTQ fwd.fastq #if rev - FASTQ2=rev.fastq + --FASTQ2 rev.fastq #end if #if $fwd.ext.startswith("fastqillumina") - QUALITY_FORMAT="Illumina" + --QUALITY_FORMAT "Illumina" #else if $fwd.ext.startswith("fastqsolexa") - QUALITY_FORMAT="Solexa" + --QUALITY_FORMAT "Solexa" #else - QUALITY_FORMAT="Standard" + --QUALITY_FORMAT "Standard" #end if - OUTPUT="${outFile}" - READ_GROUP_NAME="${read_group_name}" - SAMPLE_NAME="${sample_name}" + --OUTPUT '${outFile}' + --READ_GROUP_NAME '${read_group_name}' + --SAMPLE_NAME '${sample_name}' #if str( $library_name ): - LIBRARY_NAME="${library_name}" + --LIBRARY_NAME '${library_name}' #end if #if str( $platform_unit ): - PLATFORM_UNIT="${platform_unit}" + --PLATFORM_UNIT '${platform_unit}' #end if #if str( $platform ): - PLATFORM="${platform}" + --PLATFORM '${platform}' #end if #if str( $sequencing_center ): - SEQUENCING_CENTER="${sequencing_center}" + --SEQUENCING_CENTER '${sequencing_center}' #end if #if str( $predicted_insert_size ): - PREDICTED_INSERT_SIZE="${predicted_insert_size}" + --PREDICTED_INSERT_SIZE '${predicted_insert_size}' #end if #if str( $comment ): - COMMENT="${comment}" + --COMMENT '${comment}' #end if #if str( $description ): - DESCRIPTION="${description}" + --DESCRIPTION '${description}' #end if #if str( $run_date ): - RUN_DATE="${run_date}" + --RUN_DATE '${run_date}' #end if - MIN_Q="${min_q}" - MAX_Q="${max_q}" - STRIP_UNPAIRED_MATE_NUMBER="${strip_unpairied_mate_number}" - ALLOW_AND_IGNORE_EMPTY_LINES="${allow_and_ignore_empty_lines}" + --MIN_Q '${min_q}' + --MAX_Q '${max_q}' + --STRIP_UNPAIRED_MATE_NUMBER '${strip_unpairied_mate_number}' + --ALLOW_AND_IGNORE_EMPTY_LINES '${allow_and_ignore_empty_lines}' - SORT_ORDER=coordinate - VALIDATION_STRINGENCY="${validation_stringency}" - QUIET=true - VERBOSITY=ERROR - ]]></command> - <inputs> - <conditional name="input_type"> - <param name="input_type_selector" type="select" label="What is your input data" help="Select between single end, paired end, and collections. See help below for full explanation of dataset types"> - <option value="se">Single end (single dataset)</option> - <option value="pe">Paired end (two datasets)</option> - <option value="pc">Paired collection</option> - </param> - <when value="se"> - <param name="fastq" type="data" format="fastq,fastq.gz" label="Input fastq file for single end data" help="FASTQ"/> - </when> - <when value="pe"> - <param name="fastq" type="data" format="fastq,fastq.gz" label="Input fastq file for the first read in paired end data" help="FASTQ"/> - <param name="fastq2" type="data" format="fastq,fastq.gz" label="Input fastq file for the second read of paired end data" help="FASTQ2"/> - </when> - <when value="pc"> - <param name="fastq" type="data_collection" collection_type="paired" format="fastq,fastq.gz" label="FASTQ paired dataset collection" help="FASTQ and FASTQ2; A collection of two datasets with forward and reverse reads. See help below on explanation of dataset collections"/> - </when> - </conditional> - - <param name="read_group_name" type="text" value="A" label="Read group name" help="READ_GROUP_NAME"/> - <param name="sample_name" type="text" value="sample-a" label="Sample name" help="SAMPLE_NAME"/> - <param name="library_name" type="text" optional="True" label="The library name" help="LIBRARY_NAME; Optional"/> - <param name="platform_unit" type="text" optional="True" label="The platform unit (often run_barcode.lane)" help="PLATFORM_UNIT; Optional"/> - <param name="platform" type="text" optional="True" label="The platform type (e.g. illumina, 454)" help="PLATFORM; Optional"/> - <param name="sequencing_center" type="text" optional="True" label="The sequencing center from which the data originated" help="SEQUENCING_CENTER; Optional"/> + --SORT_ORDER coordinate + --VALIDATION_STRINGENCY '${validation_stringency}' + --QUIET true + --VERBOSITY ERROR - <param name="predicted_insert_size" type="integer" min="0" max="100000" optional="True" label="Predicted median insert size, to insert into the read group header" help="PREDICTED_INSERT_SIZE; Optional"/> - <param name="comment" type="text" optional="True" label="Comment to include in the output dataset's header" help="COMMENT; Optional"/> - <param name="description" type="text" optional="True" label="Optional description information" help="DESCRIPTION; Optional"/> - <param name="run_date" optional="True" type="text" label="Run date" help="RGDT; Optional; Format=YYYY-MM-DD (eg 1997-07-16)"/> - <param name="min_q" type="integer" value="0" min="0" max="100" label="Minimum quality allowed in the input fastq" help="MIN_Q; An exception will be thrown if a quality is less than this value; default=0"/> - <param name="max_q" type="integer" value="93" min="0" max="100" label="Minimum quality allowed in the input fastq" help="MAX_Q; An exception will be thrown if a quality is greater than this value; default=93"/> - <param name="strip_unpairied_mate_number" type="boolean" truevalue="true" falsevalue="false" label="If true and this is an unpaired fastq any occurance of '/1' will be removed from the end of a read name" help="STRIP_UNPAIRED_MATE_NUMBER; default=false"/> - <param name="allow_and_ignore_empty_lines" type="boolean" truevalue="true" falsevalue="false" label="Allow (and ignore) empty lines" help="ALLOW_AND_IGNORE_EMPTY_LINES; default=false"/> - - <expand macro="VS" /> - - </inputs> - - <outputs> - <data format="unsorted.bam" name="outFile" label="${tool.name} on ${on_string}: reads as unaligned BAM"/> - </outputs> - - <tests> - <test> - <param name="input_type_selector" value="pe" /> - <param name="read_group_name" value="A" /> - <param name="sample_name" value="sample-a" /> - <param name="library_name" value="A"/> - <param name="platform_unit" value="A"/> - <param name="platform" value="Illumina"/> - <param name="sequencing_center" value="A"/> - <param name="predicted_insert_size" value="300"/> - <param name="comment" value="A"/> - <param name="description" value="A"/> - <param name="run_date" value="2014-10-10"/> - <param name="min_q" value="0" /> - <param name="max_q" value="93" /> - <param name="strip_unpairied_mate_number" value="False" /> - <param name="allow_and_ignore_empty_lines" value="False" /> - <param name="validation_stringency" value="LENIENT"/> - <param name="fastq" value="picard_FastqToSam_read1.fq.gz" ftype="fastq.gz" /> - <param name="fastq2" value="picard_FastqToSam_read2.fq.gz" ftype="fastq.gz" /> - <output name="outFile" file="picard_FastqToSam_test1.bam" ftype="unsorted.bam" lines_diff="4"/> - </test> - </tests> - - <help> + ]]></command> + <inputs> + <conditional name="input_type"> + <param name="input_type_selector" type="select" label="What is your input data" help="Select between single end, paired end, and collections. See help below for full explanation of dataset types"> + <option value="se">Single end (single dataset)</option> + <option value="pe">Paired end (two datasets)</option> + <option value="pc">Paired collection</option> + </param> + <when value="se"> + <param name="fastq" type="data" format="fastq,fastq.gz" label="Input fastq file for single end data" help="FASTQ"/> + </when> + <when value="pe"> + <param name="fastq" type="data" format="fastq,fastq.gz" label="Input fastq file for the first read in paired end data" help="FASTQ"/> + <param name="fastq2" type="data" format="fastq,fastq.gz" label="Input fastq file for the second read of paired end data" help="FASTQ2"/> + </when> + <when value="pc"> + <param name="fastq" type="data_collection" collection_type="paired" format="fastq,fastq.gz" label="FASTQ paired dataset collection" help="FASTQ and FASTQ2; A collection of two datasets with forward and reverse reads. See help below on explanation of dataset collections"/> + </when> + </conditional> + <param name="read_group_name" type="text" value="A" label="Read group name" help="READ_GROUP_NAME"/> + <param name="sample_name" type="text" value="sample-a" label="Sample name" help="SAMPLE_NAME"/> + <param name="library_name" type="text" optional="True" label="The library name" help="LIBRARY_NAME; Optional"/> + <param name="platform_unit" type="text" optional="True" label="The platform unit (often run_barcode.lane)" help="PLATFORM_UNIT; Optional"/> + <param name="platform" type="text" optional="True" label="The platform type (e.g. illumina, 454)" help="PLATFORM; Optional"/> + <param name="sequencing_center" type="text" optional="True" label="The sequencing center from which the data originated" help="SEQUENCING_CENTER; Optional"/> + <param name="predicted_insert_size" type="integer" min="0" max="100000" optional="True" label="Predicted median insert size, to insert into the read group header" help="PREDICTED_INSERT_SIZE; Optional"/> + <param name="comment" type="text" optional="True" label="Comment to include in the output dataset's header" help="COMMENT; Optional"/> + <param name="description" type="text" optional="True" label="Optional description information" help="DESCRIPTION; Optional"/> + <param name="run_date" optional="True" type="text" label="Run date" help="RGDT; Optional; Format=YYYY-MM-DD (eg 1997-07-16)"/> + <param name="min_q" type="integer" value="0" min="0" max="100" label="Minimum quality allowed in the input fastq" help="MIN_Q; An exception will be thrown if a quality is less than this value; default=0"/> + <param name="max_q" type="integer" value="93" min="0" max="100" label="Minimum quality allowed in the input fastq" help="MAX_Q; An exception will be thrown if a quality is greater than this value; default=93"/> + <param name="strip_unpairied_mate_number" type="boolean" truevalue="true" falsevalue="false" label="If true and this is an unpaired fastq any occurance of '/1' will be removed from the end of a read name" help="STRIP_UNPAIRED_MATE_NUMBER; default=false"/> + <param name="allow_and_ignore_empty_lines" type="boolean" truevalue="true" falsevalue="false" label="Allow (and ignore) empty lines" help="ALLOW_AND_IGNORE_EMPTY_LINES; default=false"/> + <expand macro="VS"/> + </inputs> + <outputs> + <data format="unsorted.bam" name="outFile" label="${tool.name} on ${on_string}: reads as unaligned BAM"/> + </outputs> + <tests> + <test> + <param name="input_type_selector" value="pe"/> + <param name="read_group_name" value="A"/> + <param name="sample_name" value="sample-a"/> + <param name="library_name" value="A"/> + <param name="platform_unit" value="A"/> + <param name="platform" value="Illumina"/> + <param name="sequencing_center" value="A"/> + <param name="predicted_insert_size" value="300"/> + <param name="comment" value="A"/> + <param name="description" value="A"/> + <param name="run_date" value="2014-10-10"/> + <param name="min_q" value="0"/> + <param name="max_q" value="93"/> + <param name="strip_unpairied_mate_number" value="False"/> + <param name="allow_and_ignore_empty_lines" value="False"/> + <param name="validation_stringency" value="LENIENT"/> + <param name="fastq" value="picard_FastqToSam_read1.fq.gz" ftype="fastq.gz"/> + <param name="fastq2" value="picard_FastqToSam_read2.fq.gz" ftype="fastq.gz"/> + <output name="outFile" file="picard_FastqToSam_test1.bam" ftype="unsorted.bam" lines_diff="4"/> + </test> + </tests> + <help> .. class:: infomark @@ -237,5 +230,5 @@ @more_info@ </help> - <expand macro="citations" /> + <expand macro="citations"/> </tool>