annotate chira_merge.xml @ 1:ce26b5a859ba draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit 6845f3b028a42acbefb07c5f59fd2e558f50a768"
author iuc
date Mon, 02 Mar 2020 13:36:40 -0500
parents 5db894671434
children 0170de5072d4
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5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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1 <tool id="chira_merge" name="ChiRA merge" version="@WRAPPER_VERSION@0">
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2 <description>merge aligned positions</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <command><![CDATA[
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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8 chira_merge.py
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9 -b '$alignments'
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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10 #if str($annotation.choice) == "yes":
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11 -g '$annotation.gtf'
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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12 #end if
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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13 -ao '$alignment_overlap'
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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14 -so '$segment_overlap'
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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15 -o ./
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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16 ]]></command>
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17
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18 <inputs>
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19 <param format="bed" name="alignments" type="data" label="Input BED file of alignments"/>
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20 <conditional name="annotation">
1
ce26b5a859ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit 6845f3b028a42acbefb07c5f59fd2e558f50a768"
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21 <param name="choice" type="select" label="Do you have an annotation in GTF format?">
0
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22 <option value="yes">Yes</option>
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23 <option value="no">No</option>
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24 </param>
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25 <when value="yes">
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26 <param format="gtf,gff" name="gtf" type="data" label="Annotations in GTF format"/>
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27 </when>
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28 <when value="no">
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29 <!-- Do nothing -->
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30 </when>
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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31 </conditional>
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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32 <param name="alignment_overlap" type="float" value="0.7" label="Overlap fraction for merging alignments" min="0" max="1"
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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33 help="Minimum fraction of BED entries that must overlap inorder to merge"/>
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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34 <param name="segment_overlap" type="float" value="0.7" label="Overlap fraction for merging mapped read positions to segments" min="0" max="1"
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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35 help="Matching read positions with greater than this fraction overlap are merged into a segment"/>
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36 </inputs>
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37 <outputs>
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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38 <data format="bed" name="segments_bed" from_work_dir="segments.bed" label="ChiRA aligned read segments on ${on_string}"/>
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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39 <data format="tabular" name="merged_bed" from_work_dir="merged.bed" label="ChiRA merged alignments on ${on_string}"/>
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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40 </outputs>
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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41
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42 <tests>
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43 <!-- Test: Map without annotation -->
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44 <test expect_num_outputs="2">
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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45 <param name="alignments" value="alignments.bed"/>
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46 <param name="choice" value="no" />
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47 <output name="segments_bed" >
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48 <assert_contents>
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49 <has_text_matching expression="ENSMUST00000160533\t69\t82\t6|1|4,ENSMUST00000160533,69,82,+,42S13M\t0\t+" />
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50 </assert_contents>
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51 </output>
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52 <output name="merged_bed" >
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53 <assert_contents>
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54 <has_text_matching expression="ENSMUST00000182010\t19\t74\t+\t6|1|1,ENSMUST00000182010,19,68,+,5S49M1S;7|9|1,ENSMUST00000182010,24,74,+,5S50M" />
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55 </assert_contents>
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56 </output>
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57 </test>
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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58 <!-- Test: Map with annotation -->
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59 <test expect_num_outputs="2">
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60 <param name="alignments" value="alignments.bed" />
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61 <param name="choice" value="yes" />
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62 <param name="gtf" value="annotation.gtf" />
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63 <output name="segments_bed" >
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64 <assert_contents>
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65 <has_text_matching expression="5\t137142331\t137142344\t6|1|4,ENSMUST00000160533,69,82,+,42S13M\t0\t-" />
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66 </assert_contents>
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67 </output>
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68 <output name="merged_bed" >
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69 <assert_contents>
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70 <has_text_matching expression="17\t39846976\t39847031\t+\t6|1|1,ENSMUST00000182010,19,68,+,5S49M1S;7|9|1,ENSMUST00000182010,24,74,+,5S50M" />
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71 </assert_contents>
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72 </output>
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73 </test>
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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74 </tests>
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75
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76 <help>
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77
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78 .. class:: infomark
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79
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80 **What it does**
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81
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82 This tool merges the overlapping aligned positions to define the read concentrated loci. If an annotation GTF file produced, the transcriptomic alignment positions are first converted to their corresponding genomic positions.
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83
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84 **Inputs**
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85
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86 * Alignments in BED format
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87 * An annotation GTF file contaning reference genomic positions.
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88
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89 **Output**
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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90
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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91 * BED file containing the alignments with reads categorized into segments depending on which part of the read is aligned.
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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92 * Tabular file containing merged alignments. 4th column contains all the alignments merged into that location.
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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93
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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94 </help>
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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95 <expand macro="citations" />
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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96 </tool>