Mercurial > repos > bgruening > bamhash
diff bamhash.xml @ 0:63f6f42d112b draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 7aa0b566d492b1830c0bd2e54ddf4a26be95f76d
author | bgruening |
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date | Thu, 17 Sep 2015 08:00:35 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bamhash.xml Thu Sep 17 08:00:35 2015 -0400 @@ -0,0 +1,162 @@ +<tool id="bamhash" name="BamHash" version="1.1"> + <description>Hash BAM and FASTQ files to verify data integrity</description> + <requirements> + <requirement type="package" version="1.1">bamhash</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + <exit_code range=":-1" /> + <regex match="Error:" /> + <regex match="Exception:" /> + </stdio> + <version_command>bamhash_checksum_fastq --version</version_command> + <command><![CDATA[ + #if $tool.tool_choice=="bam": + #for $counter, $file in enumerate($tool.input_bam): + ln -s "${file}" "${counter}.bam" ## 1.bam ... 2.bam + && + #end for + bamhash_checksum_bam + $tool.noQuality_bam + $tool.noPaired_bam + #for $counter, $filename in enumerate($tool.input_bam): + "${counter}.bam" + #end for + #elif $tool.tool_choice=="fastq": + #for $counter, $file in enumerate($tool.input_fastq): + ln -s "${file}" "${counter}.fastq" ## 1.fastq ... 2.fastq + && + #end for + bamhash_checksum_fastq + $tool.noQuality_fastq + $tool.noPaired_fastq + #for $counter, $filename in enumerate($tool.input_fastq): + "${counter}.fastq" + #end for + #elif $tool.tool_choice=="fasta": + #for $counter, $file in enumerate($tool.input_fasta): + ln -s "${file}" "${counter}.fasta" ## 1.fasta ... 2.fasta + && + #end for + bamhash_checksum_fasta + #for $counter, $filename in enumerate($tool.input_fasta): + "${counter}.fasta" + #end for + #end if + $readnames + > output.txt + ]]></command> + <inputs> + <conditional name="tool"> + <param name="tool_choice" type="select" label="Choose file type:" + help=""> + <option value="bam">BAM file(s)</option> + <option value="fastq">FASTQ file(s)</option> + <option value="fasta">FASTA file(s)</option> + </param> + <when value="bam"> + <param name="input_bam" multiple="True" type="data" format="bam" label="Input file in BAM format"/> + <param name="noQuality_bam" type="boolean" checked="false" truevalue="--no-quality" + falsevalue="" + label="Ignore read quality?" + help="Do not use read quality as part of checksum. (--no-quality)"/> + <param name="noPaired_bam" type="boolean" checked="false" truevalue="--no-paired" + falsevalue="" + label="Bam files were not generated with paired-end reads?" + help="(--no-paired)" /> + </when> + <when value="fasta"> + <param name="input_fasta" multiple="True" type="data" format="fasta" label="Input file in FASTA format"/> + </when> + <when value="fastq"> + <param name="input_fastq" multiple="True" type="data" format="fastq" label="Input file in FASTQ format"/> + <param name="noQuality_fastq" type="boolean" checked="false" truevalue="--no-quality" + falsevalue="" + label="Ignore read quality?" + help="Do not use read quality as part of checksum. (--no-quality)"/> + <param name="noPaired_fastq" type="boolean" checked="false" truevalue="--no-paired" + falsevalue="" + label="List of fastq files are not paired-end reads?" + help="(--no-paired)" /> + </when> + </conditional> + <param name="readnames" type="boolean" checked="false" truevalue="--no-readnames" + falsevalue="" + label="Ignore readnames?" + help="Do not use read names as part of checksum. (--no-readnames)"/> + + </inputs> + <outputs> + <data name="output" format="txt" from_work_dir="./output.txt" + label="${tool.name} on ${on_string}"> + </data> + </outputs> + <tests> + <test> + <param name="input_bam" value="Example.bam" ftype="bam"/> + <param name="tool_choice" value="bam"/> + <output name="output" file="output1_bam.txt" ftype="txt"/> + </test> + <test> + <param name="input_fasta" value="UnAligSeq24606.fasta" ftype="fasta"/> + <param name="tool_choice" value="fasta"/> + <param name="readnames" value="--no-readnames"/> + <output name="output" file="output2_fasta.txt" ftype="txt"/> + </test> + <test> + <param name="input_fastq" value="1_mismatch.fastq,2_mismatch.fastq" ftype="fastq"/> + <param name="tool_choice" value="fastq"/> + <param name="noQuality" value="--no-quality"/> + <output name="output" file="output3_fastq.txt" ftype="txt"/> + </test> + <test> + <param name="input_fastq" value="1_mismatch.fastq,2_mismatch.fastq" ftype="fastq"/> + <param name="tool_choice" value="fastq"/> + <output name="output" file="output4_fastq.txt" ftype="txt"/> + </test> + </tests> + <help><![CDATA[ + +**WHAT IT DOES** + +Hash BAM and FASTQ files to verify data integrity + +For each pair of reads in a BAM or FASTQ file we compute a hash value composed of the readname, +whether it is first or last in pair, sequence and quality value. All the hash values are summed +up so the result is independent of the ordering within the files. The result can be compared to +verify that the pair of FASTQ files contain the same read information as the aligned BAM file. + +----- + +**BAM** + +processes a number of BAM files. BAM files are assumed to contain paired end reads. +If you run with --no-paired it treats all reads as single end and displays a warning if any read is marked as "second in pair" in the BAM file. + +----- + +**FASTA** + +processes a number of FASTA files. All FASTA files are assumed to be single end reads with no quality information. +To compare to a BAM file, run bamhash_checksum_bam --no-paired --no-quality + +----- + + +**FASTQ** + +processes a number of FASTQ files. FASTQ files are assumed to contain paired end reads, +such that the first two files contain the first pair of reads, etc. If any of the read names in the two pairs don't match the program exits with failure. + + +----- + + +**BamHash** is a Free and Open Source Software, see more details on the BamHash github_ Website. + +.. _github: https://github.com/DecodeGenetics/BamHash + + ]]></help> + <citations> + </citations> +</tool>