Mercurial > repos > yufei-luo > s_mart
diff smart_toolShed/SMART/galaxy/mapperAnalyzer.xml @ 0:e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
| author | yufei-luo |
|---|---|
| date | Thu, 17 Jan 2013 10:52:14 -0500 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/smart_toolShed/SMART/galaxy/mapperAnalyzer.xml Thu Jan 17 10:52:14 2013 -0500 @@ -0,0 +1,186 @@ +<tool id="mapperAnalyzer" name="mapper analyzer"> + <description>Read the output of an aligner, print statistics and possibly translate into BED or GBrowse formats. </description> + <command interpreter="python"> + ../Java/Python/mapperAnalyzer.py -i $formatType.inputFileName1 + #if $formatType.FormatInputFileName1 == 'bed': + -f bed + #elif $formatType.FormatInputFileName1 == 'gff3': + -f gff3 + #elif $formatType.FormatInputFileName1 == 'sam': + -f sam + #elif $formatType.FormatInputFileName1 == 'bam': + -f bam + #elif $formatType.FormatInputFileName1 == 'seqmap': + -f seqmap + #end if + + -q $formatType2.inputFileName2 + #if $formatType2.FormatInputFileName2 == 'fasta': + -k fasta + #elif $formatType2.FormatInputFileName2 == 'fastq': + -k fastq + #end if + + + #if $optionnumber.number == 'Yes': + -n $optionnumber.numberVal + #end if + #if $optionsize.size == 'Yes': + -s $optionsize.sizeVal + #end if + #if $optionidentity.identity == 'Yes': + -d $optionidentity.identityVal + #end if + #if $optionmismatch.mismatch == 'Yes': + -m $optionmismatch.mismatchVal + #end if + #if $optiongap.gap == 'Yes': + -p $optiongap.gapVal + #end if + #if $optiontitle.title == 'Yes': + -t $optiontitle.titleVal + #end if + #if $optionappend.append == 'Yes': + -a $optionappend.appendfile + #end if + + $merge + $remove + $remain + -o $outputFileGFF + </command> + + <inputs> + <conditional name="formatType"> + <param name="FormatInputFileName1" type="select" label="Input File mapping Format"> + <option value="bed">bed</option> + <option value="gff3">gff3</option> + <option value="sam">sam</option> + <option value="bam">bam</option> + <option value="seqmap" selected="true">seqmap</option> + </param> + <when value="bed"> + <param name="inputFileName1" format="bed" type="data" label="Input File"/> + </when> + <when value="gff3"> + <param name="inputFileName1" format="gff3" type="data" label="Input File"/> + </when> + <when value="sam"> + <param name="inputFileName1" format="sam" type="data" label="Input File"/> + </when> + <when value="bam"> + <param name="inputFileName1" format="bam" type="data" label="Input File"/> + </when> + <when value="seqmap"> + <param name="inputFileName1" format="seqmap" type="data" label="Input File"/> + </when> + </conditional> + + <conditional name="formatType2"> + <param name="FormatInputFileName2" type="select" label="Reference sequence File Format"> + <option value="fasta" selected="true">fasta</option> + <option value="fastq">fastq</option> + </param> + <when value="fasta"> + <param name="inputFileName2" format="fasta" type="data" label="Reference sequence File Format"/> + </when> + <when value="fastq"> + <param name="inputFileName2" format="fastq" type="data" label="Reference sequence File Format"/> + </when> + </conditional> + + + <conditional name="optionnumber"> + <param name="number" type="select" label="max. number of occurrences of a sequence"> + <option value="Yes">Yes</option> + <option value="No" selected="true">No</option> + </param> + <when value="Yes"> + <param name="numberVal" type="integer" value="0"/> + </when> + <when value="No"> + </when> + </conditional> + + <conditional name="optionsize"> + <param name="size" type="select" label="minimum pourcentage of size "> + <option value="Yes">Yes</option> + <option value="No" selected="true">No</option> + </param> + <when value="Yes"> + <param name="sizeVal" type="integer" value="0"/> + </when> + <when value="No"> + </when> + </conditional> + + <conditional name="optionidentity"> + <param name="identity" type="select" label="minimum pourcentage of identity "> + <option value="Yes">Yes</option> + <option value="No" selected="true">No</option> + </param> + <when value="Yes"> + <param name="identityVal" type="integer" value="0"/> + </when> + <when value="No"> + </when> + </conditional> + + <conditional name="optionmismatch"> + <param name="mismatch" type="select" label="maximum number of mismatches"> + <option value="Yes">Yes</option> + <option value="No" selected="true">No</option> + </param> + <when value="Yes"> + <param name="mismatchVal" type="integer" value="0"/> + </when> + <when value="No"> + </when> + </conditional> + + <conditional name="optiongap"> + <param name="gap" type="select" label="maximum number of gaps"> + <option value="Yes">Yes</option> + <option value="No" selected="true">No</option> + </param> + <when value="Yes"> + <param name="gapVal" type="integer" value="0"/> + </when> + <when value="No"> + </when> + </conditional> + + <conditional name="optiontitle"> + <param name="title" type="select" label="title of the plots "> + <option value="Yes">Yes</option> + <option value="No" selected="true">No</option> + </param> + <when value="Yes"> + <param name="titleVal" type="text" value="title of the UCSC track" /> + </when> + <when value="No"> + </when> + </conditional> + + <conditional name="optionappend"> + <param name="append" type="select" label="append to GFF3 file"> + <option value="Yes">Yes</option> + <option value="No" selected="true">No</option> + </param> + <when value="Yes"> + <param name="appendfile" type="data" format="gff3" label="append a file"/> + </when> + <when value="No"> + </when> + </conditional> + + <param name="merge" type="boolean" truevalue="-e" falsevalue="" checked="false" label="merge exons when introns are short "/> + <param name="remove" type="boolean" truevalue="-x" falsevalue="" checked="false" label="remove transcripts when exons are short"/> + <param name="remain" type="boolean" truevalue="-r" falsevalue="" checked="false" label="print the unmatched sequences "/> + </inputs> + + <outputs> + <data name="outputFileGFF" format="gff3" label="[mapperAnalyzer] out file"/> + </outputs> + +</tool>