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planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
author wolma
date Sat, 11 Nov 2017 16:39:44 -0500
parents 85576338fbcf
children
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1 <tool id="mimodd_sort" name="MiModD Sort" version="@MIMODD_WRAPPER_VERSION@">
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2 <description>takes a SAM/BAM dataset and generates a coordinate/name-sorted copy</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 <expand macro="stdio" />
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8 <expand macro="version_command" />
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9 <command>
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10 mimodd sort '$input.ifile'
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11 -o '$ofile' --iformat $input.iformat --oformat $oformat $by_name
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12 </command>
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14 <inputs>
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15 <conditional name="input">
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16 <param name="iformat" type="select" label="Input data format">
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17 <option value="bam">bam</option>
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18 <option value="sam">sam</option>
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19 </param>
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20 <when value="bam">
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21 <param name="ifile" type="data" format="bam"
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22 label="BAM input dataset to sort" />
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23 </when>
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24 <when value="sam">
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25 <param name="ifile" type="data" format="sam"
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26 label="SAM input dataset to sort" />
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27 </when>
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28 </conditional>
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29 <param name="oformat" type="select" label="Output format for the sorted data">
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30 <option value="bam">bam</option>
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31 <option value="sam">sam</option>
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32 </param>
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33 <param name="by_name" type="boolean" truevalue="-n" falsevalue="" checked="false"
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34 label="Sort by read names instead of coordinates"
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35 help="A less common option, but necessary, e.g., if you want to re-align coordinate sorted paired-end reads with the MiModD Read Alignment Tool or other NGS mapping tools." />
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36 </inputs>
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37
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38 <outputs>
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39 <data name="ofile" format="bam"
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40 label="Sorted output from MiModd ${tool.name} on ${on_string}">
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41 <change_format>
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42 <when input="oformat" value="sam" format="sam" />
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43 </change_format>
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44 </data>
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45 </outputs>
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46
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47 <tests>
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48 <test>
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49 <conditional name="input">
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50 <param name="iformat" value="sam" />
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51 <param name="ifile" value="header_only.sam" />
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52 </conditional>
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53 <param name="oformat" value="bam" />
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54 <assert_command>
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55 <not_has_text text="-n" />
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56 </assert_command>
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57 <output name="ofile" ftype="bam" file="so_coordinate.bam" />
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58 </test>
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59 <test>
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60 <conditional name="input">
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61 <param name="iformat" value="bam" />
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62 <param name="ifile" value="header_only.bam" />
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63 </conditional>
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64 <param name="oformat" value="sam" />
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65 <param name="by_name" value="true" />
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66 <assert_command>
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67 <has_text text=" -n" />
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68 </assert_command>
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69 <output name="ofile" ftype="sam" file="so_queryname.sam" />
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70 </test>
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71 </tests>
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72
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73 <help><![CDATA[
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74 .. class:: infomark
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75
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76 **What it does**
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77
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78 The tool sorts an aligned reads input dataset, typically by the reference
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79 genome coordinates that the reads have been mapped to.
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80
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81 Coordinate-sorted input files are expected by most downstream MiModD tools, but
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82 note that the *MiModD Read Alignment* produces coordinate-sorted output by
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83 default and it is only necessary to sort files that come from other sources or
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84 from *MiModD Read Alignment* jobs with a custom sort order.
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85
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86 The option *Sort by read names instead of coordinates* is useful if you want to
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87 re-align coordinate-sorted paired-end data. In *paired-end mode*, the
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88 *MiModD Read Alignment* tool expects the reads in the input file to be arranged
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89 in read pairs, *i.e.*, the forward read information of a pair must be followed
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90 immediately by its reverse mate information, which is typically not the case in
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91 coordinate-sorted data. Resorting such data by read names fixes this problem.
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92
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93 @HELP_FOOTER@
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94 ]]></help>
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95 <expand macro="citations" />
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96 </tool>
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97