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annotate macs2_predictd.xml @ 59:ea526bc73f8a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 30858afbdbe0223d07d2936a8469295bcbeda786
author iuc
date Mon, 15 Oct 2018 06:48:49 -0400
parents 8f6b37d29df5
children 644444825ef9
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1 <tool id="macs2_predictd" name="MACS2 predictd" version="@VERSION_STRING@.0">
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2 <description>Predict 'd' or fragment size from alignment results</description>
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3 <macros>
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4 <import>macs2_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <expand macro="stdio" />
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8 <expand macro="version_command" />
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9 <command><![CDATA[
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10 @home_dir@
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11 macs2 predictd
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12
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13 -i ${ ' '.join(["'%s'" % $x for $x in $infiles ]) }
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14 @tag_size@
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15 @effective_genome_size@
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16 --bw '${ band_width }'
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17 @mfold_command@
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18
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19 ## remove the timepoint and strip the output
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20 2>&1 | awk -F: '{print $4}' | awk '{$1=$1}1'
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22 > '${ outfile }'
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24 &&
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26 Rscript predictd
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27 ]]></command>
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28 <inputs>
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29 <param name="infiles" type="data" format="bam,sam,bed" multiple="True"
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30 label="ChIP-seq alignment file"
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31 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)" />
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32 <expand macro="conditional_effective_genome_size" />
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33 <expand macro="tag_size" />
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34 <expand macro="band_width" />
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35 <expand macro="mfold_options" />
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36 </inputs>
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38 <outputs>
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39 <data name="outfile" format="txt" label="${tool.name} on ${on_string} - d value" />
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40 <data name="outfile_image" from_work_dir="predictd_model.pdf" format="pdf" label="${tool.name} on ${on_string} - X-correlation image" />
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41 </outputs>
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42 <tests>
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43 <test>
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44 <param name="infiles" value="Control_200K.bed,ChIP_200K.bed" ftype="bed" />
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45 <param name="effective_genome_size_options_selector" value="user_defined" />
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46 <param name="gsize" value="3300000000" />
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47 <param name="tsize" value=""/>
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48 <param name="band_width" value="300"/>
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49 <param name="lower" value="5"/>
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50 <param name="upper" value="50"/>
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51 <output name="outfile">
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52 <assert_contents>
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53 <has_line line="# predicted fragment length is 284 bps" />
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54 </assert_contents>
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55 </output>
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56 <output name="outfile_image" file="predictd_on_ChIP_200K_and_Control_200K.pdf" compare="sim_size"/>
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57 </test>
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58 </tests>
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59 <help>
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60 <![CDATA[
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61 **What it does**
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62
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63 This is **predictd** utility from the MACS2_ Package. It predicts the *d* value or fragment size from alignment results.
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64
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65 .. _MACS2: https://github.com/taoliu/MACS
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67 @citation@
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68 ]]>
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70 </help>
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71 <expand macro="citations" />
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72 </tool>