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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 7bd4238efae0d755b6a0dfff8daa43a228f18d96
author iuc
date Mon, 16 Oct 2023 13:18:37 +0000
parents 640d3af5d833
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1 <tool id="macs2_predictd" name="MACS2 predictd" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
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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="bio_tools"/>
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7 <expand macro="requirements"/>
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8 <expand macro="stdio" />
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9 <expand macro="version_command" />
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10 <command><![CDATA[
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11 @home_dir@
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12 macs2 predictd
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14 -i ${ ' '.join(["'%s'" % $x for $x in $infiles ]) }
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15 @tag_size@
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16 @effective_genome_size@
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17 --bw '${ band_width }'
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18 @mfold_command@
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19 --d-min $d_min
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20 @buffer_size@
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21
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22 ## remove the timepoint and strip the output
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23 2>&1 | awk -F: '{print $4}' | awk '{$1=$1}1'
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25 > '${ outfile }'
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27 &&
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28
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29 Rscript predictd
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30 ]]></command>
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31 <inputs>
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32 <param name="infiles" type="data" format="bam,bed" multiple="True"
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33 label="ChIP-seq alignment file"
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34 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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35 <expand macro="conditional_effective_genome_size" />
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36 <expand macro="tag_size" />
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37 <expand macro="band_width" />
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38 <expand macro="mfold_options" />
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39 <expand macro="fragment_size"/>
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40 <expand macro="buffer_size"/>
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41 </inputs>
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42
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43 <outputs>
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44 <data name="outfile" format="txt" label="${tool.name} on ${on_string} - d value" />
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45 <data name="outfile_image" from_work_dir="predictd_model.pdf" format="pdf" label="${tool.name} on ${on_string} - X-correlation image" />
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46 </outputs>
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47 <tests>
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48 <test>
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49 <param name="infiles" value="Control_200K.bed,ChIP_200K.bed" ftype="bed" />
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50 <param name="effective_genome_size_options_selector" value="user_defined" />
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51 <param name="gsize" value="3300000000" />
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52 <param name="tsize" value=""/>
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53 <param name="band_width" value="300"/>
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54 <param name="lower" value="5"/>
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55 <param name="upper" value="50"/>
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56 <assert_command>
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57 <has_text text="--buffer-size"/>
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58 <has_text text="--d-min"/>
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59 </assert_command>
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60 <output name="outfile">
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61 <assert_contents>
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62 <has_line line="# predicted fragment length is 284 bps" />
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63 </assert_contents>
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64 </output>
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65 <output name="outfile_image" file="predictd_on_ChIP_200K_and_Control_200K.pdf" compare="sim_size" ftype="pdf"/>
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66 </test>
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67 </tests>
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68 <help>
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69 <![CDATA[
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70 **What it does**
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71
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72 This is **predictd** utility from the MACS2_ Package. It predicts the *d* value or fragment size from alignment results.
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73
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74 .. _MACS2: https://github.com/taoliu/MACS
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75
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76 @citation@
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77 ]]>
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78
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79 </help>
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80 <expand macro="citations" />
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81 </tool>