[2] | 1 | <tool id="wig_to_bigWig" name="Wig to bigWig" version="1.0.0"> |
---|
| 2 | <description>converter</description> |
---|
| 3 | <command>grep -v "^track" $input1 | wigToBigWig stdin $chromInfo $out_file1 -blockSize=$blockSize -itemsPerSlot=$itemsPerSlot $clip $unc 2>&1 || echo "Error running wigToBigWig." >&2</command> |
---|
| 4 | <requirements> |
---|
| 5 | <requirement type="package">ucsc_tools</requirement> |
---|
| 6 | </requirements> |
---|
| 7 | <inputs> |
---|
| 8 | <param format="wig" name="input1" type="data" label="Convert"> |
---|
| 9 | <validator type="unspecified_build" /> |
---|
| 10 | </param> |
---|
| 11 | <param name="blockSize" size="4" type="integer" value="256" label="Items to bundle in r-tree" help="Default is 256 (blockSize)" /> |
---|
| 12 | <param name="itemsPerSlot" size="4" type="integer" value="1024" label="Data points bundled at lowest level" help="Default is 1024 (itemsPerSlot)" /> |
---|
| 13 | <param name="clip" type="boolean" truevalue="-clip" falsevalue="" checked="False" label="Clip chromosome positions" help="Issue warning messages rather than dying if wig file contains items off end of chromosome. (clip)"/> |
---|
| 14 | <param name="unc" type="boolean" truevalue="-unc" falsevalue="" checked="False" label="Do not use compression" help="(unc)"/> |
---|
| 15 | </inputs> |
---|
| 16 | <outputs> |
---|
| 17 | <data format="bigwig" name="out_file1" /> |
---|
| 18 | </outputs> |
---|
| 19 | <tests> |
---|
| 20 | <test> |
---|
| 21 | <param name="input1" value="2.wig" dbkey="hg17" /> |
---|
| 22 | <param name="blockSize" value="256" /> |
---|
| 23 | <param name="itemsPerSlot" value="1024" /> |
---|
| 24 | <param name="clip" value="False" /> |
---|
| 25 | <param name="unc" value="False" /> |
---|
| 26 | <output name="out_file1" file="2.bigwig"/> |
---|
| 27 | </test> |
---|
| 28 | </tests> |
---|
| 29 | <help> |
---|
| 30 | **Syntax** |
---|
| 31 | |
---|
| 32 | This tool converts wiggle data into bigWig type. |
---|
| 33 | |
---|
| 34 | - **Wiggle format**: The .wig format is line-oriented. Wiggle data is preceded by a UCSC track definition line. Following the track definition line is the track data, which can be entered in three different formats described below. |
---|
| 35 | |
---|
| 36 | - **BED format** with no declaration line and four columns of data:: |
---|
| 37 | |
---|
| 38 | chromA chromStartA chromEndA dataValueA |
---|
| 39 | chromB chromStartB chromEndB dataValueB |
---|
| 40 | |
---|
| 41 | - **variableStep** two column data; started by a declaration line and followed with chromosome positions and data values:: |
---|
| 42 | |
---|
| 43 | variableStep chrom=chrN [span=windowSize] |
---|
| 44 | chromStartA dataValueA |
---|
| 45 | chromStartB dataValueB |
---|
| 46 | |
---|
| 47 | - **fixedStep** single column data; started by a declaration line and followed with data values:: |
---|
| 48 | |
---|
| 49 | fixedStep chrom=chrN start=position step=stepInterval [span=windowSize] |
---|
| 50 | dataValue1 |
---|
| 51 | dataValue2 |
---|
| 52 | |
---|
| 53 | </help> |
---|
| 54 | </tool> |
---|