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annotate macs2_randsample.xml @ 18:640d3af5d833 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e8307adcc6ee9245fa2bb9ecb6de1cbe008dc2c3"
author iuc
date Sat, 02 Apr 2022 21:37:38 +0000
parents 424aefbd7777
children 86e2413cf3f8
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640d3af5d833 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e8307adcc6ee9245fa2bb9ecb6de1cbe008dc2c3"
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1 <tool id="macs2_randsample" name="MACS2 randsample" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
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2 <description>Randomly sample number or percentage of total reads</description>
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3 <expand macro="bio_tools"/>
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4 <macros>
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5 <import>macs2_macros.xml</import>
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6 </macros>
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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 randsample
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13 -i '${ infile }'
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14 -o '${ outfile }'
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15 --seed '${ seed }'
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17 --format '${ infile.extension.upper() }'
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18
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19 @tag_size@
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20
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21 #if $method_options.method_options_selector == 'percentage':
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22 --percentage '${ method_options.percentage }'
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23 #else:
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24 --number '${ method_options.number }'
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25 #end if
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26 ]]></command>
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27 <inputs>
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28 <param name="infile" type="data" format="bam,bed" label="Sequencing alignment file" />
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29 <expand macro="tag_size" />
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30 <conditional name="method_options">
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31 <param name="method_options_selector" type="select" label="Select action to be performed">
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32 <option value="percentage" selected="true">Percentage</option>
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33 <option value="number">Number</option>
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34 </param>
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35 <when value="percentage">
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36 <param name="percentage" type="float" value="80.0" label="Percentage of tags you want to keep" help="Percentage of tags you want to keep. Input 80.0 for 80%.(--percentage)"/>
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37 </when>
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38 <when value="number">
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39 <param name="number" type="integer" value="800000" label="Number of tags you want to keep" help="Note that the number of tags in output is approximate as the number specified here (--number)" />
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40 </when>
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41 </conditional>
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42 <param name="seed" type="integer" value="1" label="Random seed number" min="0" help="Set the random seed while down sampling data. Must be a positive integer in order to be effective. (--seed)"/>
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43 </inputs>
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44 <outputs>
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45 <data name="outfile" format="bed" label="${tool.name} on ${on_string}" />
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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="infile" value="ChIP_200K.bed" ftype="bed" />
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50 <param name="method_options_selector" value="percentage" />
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51 <param name="percentage" value="80.0" />
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52 <param name="seed" value="1" />
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53 <output name="outfile">
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54 <assert_contents>
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55 <has_text text="27179762" />
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56 <has_text text="4441986" />
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57 <has_size value="4787911" delta="500"/>
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58 </assert_contents>
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59 </output>
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60 </test>
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61 </tests>
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62 <help>
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63 <![CDATA[
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64 **What it does**
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65
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66 This is **randsample** utility from the MACS2_ Package. It randomly samples reads by number or percentage from an input file.
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67
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68 .. _MACS2: https://github.com/taoliu/MACS
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70 @citation@
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71 ]]>
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72 </help>
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73 <expand macro="citations" />
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74 </tool>