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annotate confindr.xml @ 4:202247a3c969 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/confindr/ commit 9e41ac63171c3e3a6fd2b4d018d0c60c9f1fbae1"
author dfornika
date Fri, 31 Jan 2020 19:09:14 +0000
parents 2ab80b982480
children
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d43117b98027 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/confindr/ commit 9e41ac63171c3e3a6fd2b4d018d0c60c9f1fbae1"
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1 <tool id="confindr" name="ConFindr" version="@VERSION@+galaxy0">
d43117b98027 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/confindr/ commit 9e41ac63171c3e3a6fd2b4d018d0c60c9f1fbae1"
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2 <description>
d43117b98027 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/confindr/ commit 9e41ac63171c3e3a6fd2b4d018d0c60c9f1fbae1"
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3 Intra-species bacterial contamination detection
d43117b98027 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/confindr/ commit 9e41ac63171c3e3a6fd2b4d018d0c60c9f1fbae1"
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4 </description>
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5 <macros>
d43117b98027 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/confindr/ commit 9e41ac63171c3e3a6fd2b4d018d0c60c9f1fbae1"
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6 <import>macros.xml</import>
d43117b98027 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/confindr/ commit 9e41ac63171c3e3a6fd2b4d018d0c60c9f1fbae1"
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7 </macros>
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8 <expand macro="requirements" />
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9 <expand macro="version_command" />
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11 <command detect_errors="exit_code"><![CDATA[
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12 mkdir input &&
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13 mkdir databases &&
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14 #if str( $reads_input.reads_input_selector ) == "paired"
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15 ln -s '$reads_input.reads_1' 'input/reads_R1.fastq' &&
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16 ln -s '$reads_input.reads_2' 'input/reads_R2.fastq' &&
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17 #end if
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18 #if str( $reads_input.reads_input_selector ) == "paired_collection"
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19 ln -s '$reads_input.reads.forward' 'input/reads_R1.fastq' &&
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20 ln -s '$reads_input.reads.reverse' 'input/reads_R2.fastq' &&
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21 #end if
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23 confindr.py
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24 --threads \${GALAXY_SLOTS:-1}
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25 --databases 'databases'
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26 --input_directory 'input'
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27 --output_name 'output'
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29 ]]></command>
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31 <inputs>
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32 <conditional name="reads_input">
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33 <param name="reads_input_selector" type="select" label="Paired-end reads or paired collection" help="Select between paired and paired collection">
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34 <option value="paired">Paired</option>
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35 <option value="paired_collection">Paired Collection</option>
d43117b98027 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/confindr/ commit 9e41ac63171c3e3a6fd2b4d018d0c60c9f1fbae1"
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36 </param>
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37 <when value="paired">
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38 <param name="reads_1" type="data" format="@INTYPES@" label="Select first set of reads" help="Specify dataset with forward reads"/>
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39 <param name="reads_2" type="data" format="@INTYPES@" label="Select second set of reads" help="Specify dataset with reverse reads"/>
d43117b98027 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/confindr/ commit 9e41ac63171c3e3a6fd2b4d018d0c60c9f1fbae1"
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40 </when>
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41 <when value="paired_collection">
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42 <param name="reads" format="@INTYPES@" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/>
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43 </when>
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44 </conditional>
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45 </inputs>
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46
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47 <outputs>
3
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48 <data name="report" format="csv" from_work_dir="output/confindr_report.csv" label="${tool.name} on ${on_string} report file" />
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49 </outputs>
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51 <tests>
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54 </tests>
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56 <help><![CDATA[
d43117b98027 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/confindr/ commit 9e41ac63171c3e3a6fd2b4d018d0c60c9f1fbae1"
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57 **What it does**
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58
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59
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60
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61 **Output**
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62
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63 ConFindr will produce a tab-seperated output file with the following outputs:
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64
3
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65 +--------------------------------+------------------------------------------------+
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66 | Column | Description |
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67 +================================+================================================+
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68 | Sample | |
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69 +--------------------------------+------------------------------------------------+
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70 | Genus | |
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71 +--------------------------------+------------------------------------------------+
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72 | ContamStatus | |
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73 +--------------------------------+------------------------------------------------+
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74 | PercentContam | |
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75 +--------------------------------+------------------------------------------------+
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76 | PercentContamStandardDeviation | |
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77 +--------------------------------+------------------------------------------------+
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78 | BasesExamined | |
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79 +--------------------------------+------------------------------------------------+
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80 | DatabaseDownloadDate | |
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81 +--------------------------------+------------------------------------------------+
0
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82
d43117b98027 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/confindr/ commit 9e41ac63171c3e3a6fd2b4d018d0c60c9f1fbae1"
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83 **Example Output**
d43117b98027 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/confindr/ commit 9e41ac63171c3e3a6fd2b4d018d0c60c9f1fbae1"
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d43117b98027 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/confindr/ commit 9e41ac63171c3e3a6fd2b4d018d0c60c9f1fbae1"
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85 ::
3
2ab80b982480 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/confindr/ commit 9e41ac63171c3e3a6fd2b4d018d0c60c9f1fbae1"
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86 Sample,Genus,NumContamSNVs,ContamStatus,PercentContam,PercentContamStandardDeviation,BasesExamined,DatabaseDownloadDate
0
d43117b98027 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/confindr/ commit 9e41ac63171c3e3a6fd2b4d018d0c60c9f1fbae1"
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d43117b98027 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/confindr/ commit 9e41ac63171c3e3a6fd2b4d018d0c60c9f1fbae1"
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d43117b98027 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/confindr/ commit 9e41ac63171c3e3a6fd2b4d018d0c60c9f1fbae1"
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89 ]]></help>
d43117b98027 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/confindr/ commit 9e41ac63171c3e3a6fd2b4d018d0c60c9f1fbae1"
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90
d43117b98027 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/confindr/ commit 9e41ac63171c3e3a6fd2b4d018d0c60c9f1fbae1"
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91 <expand macro="citations"/>
d43117b98027 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/confindr/ commit 9e41ac63171c3e3a6fd2b4d018d0c60c9f1fbae1"
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92 </tool>