Mercurial > repos > iuc > macs2
comparison macs2_predictd.xml @ 0:fe62ba547975 draft
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| author | iuc |
|---|---|
| date | Wed, 11 Feb 2015 10:18:02 -0500 |
| parents | |
| children | bfe57d6e0c4c |
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| -1:000000000000 | 0:fe62ba547975 |
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| 1 <tool id="macs2_predictd" name="MACS2 predictd" version="@VERSION_STRING@.0"> | |
| 2 <description>Predict 'd' or fragment size from alignment results</description> | |
| 3 <expand macro="requirements"> | |
| 4 <requirement type="package" version="3.0.1">R_3_0_1</requirement> | |
| 5 <requirement type="package" version="4.1.0">gnu_awk</requirement> | |
| 6 </expand> | |
| 7 <expand macro="version_command" /> | |
| 8 <macros> | |
| 9 <import>macs2_macros.xml</import> | |
| 10 </macros> | |
| 11 <command> | |
| 12 macs2 predictd | |
| 13 -i ${ ' '.join( map( lambda x:'"%s"' % ( x ), $infiles ) ) } | |
| 14 @tag_size@ | |
| 15 @effective_genome_size@ | |
| 16 --bw "${ band_width }" | |
| 17 --mfold "${ mfoldlo }" "${ mfoldhi }" | |
| 18 | |
| 19 ## remove the timepoint and strip the output | |
| 20 2>&1 | awk -F: '{print $4}' | awk '{$1=$1}1' | |
| 21 | |
| 22 > "${ outfile }" | |
| 23 | |
| 24 && | |
| 25 | |
| 26 Rscript predictd | |
| 27 </command> | |
| 28 <expand macro="stdio" /> | |
| 29 <inputs> | |
| 30 <param name="infiles" type="data" format="bam,sam,bed" multiple="True" label="ChIP-seq alignment file" help="If multiple files are given, then they will all be read and combined. Note that pair-end data is not supposed to work with this command. (-i)" /> | |
| 31 <expand macro="conditional_effective_genome_size" /> | |
| 32 <expand macro="tag_size" /> | |
| 33 <expand macro="band_width" /> | |
| 34 | |
| 35 <param name="mfoldlo" type="integer" label="Fold-enrichment lower limit" value="5" | |
| 36 help="Select the regions with MFOLD high-confidence enrichment ratio against background to build model (--mfold)"/> | |
| 37 <param name="mfoldhi" type="integer" label="Fold-enrichment upper-limit" value="50" | |
| 38 help="Select the regions with MFOLD high-confidence enrichment ratio against background to build model (--mfold)"/> | |
| 39 | |
| 40 </inputs> | |
| 41 | |
| 42 <outputs> | |
| 43 <data name="outfile" format="txt" label="${tool.name} on ${on_string} - d value" /> | |
| 44 <data name="outfile_image" from_work_dir="predictd_model.pdf" format="pdf" label="${tool.name} on ${on_string} - X-correlation image" /> | |
| 45 </outputs> | |
| 46 <tests> | |
| 47 <test> | |
| 48 <param name="infiles" value="Control_200K.bed,ChIP_200K.bed" ftype="bed" /> | |
| 49 <param name="effective_genome_size_options_selector" value="user_defined" /> | |
| 50 <param name="gsize" value="3300000000" /> | |
| 51 <param name="tsize" value="-1.0"/> | |
| 52 <param name="band_width" value="300"/> | |
| 53 <param name="mfoldlo" value="5"/> | |
| 54 <param name="mfoldhi" value="50"/> | |
| 55 <output name="outfile" file="predictd_on_ChIP_200K_and_Control_200K.txt"/> | |
| 56 <output name="outfile_image" file="predictd_on_ChIP_200K_and_Control_200K.pdf" compare="sim_size"/> | |
| 57 </test> | |
| 58 </tests> | |
| 59 <help> | |
| 60 **What it does** | |
| 61 | |
| 62 predictd from macs2 | |
| 63 | |
| 64 | |
| 65 Note that pair-end data is not supposed to work with this command. | |
| 66 | |
| 67 | |
| 68 @citation@ | |
| 69 </help> | |
| 70 <expand macro="citations" /> | |
| 71 </tool> |