Mercurial > repos > iuc > obi_sort

annotate obisort.xml @ 4:b6d9ea2fb41b draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
author iuc
date Wed, 20 Mar 2024 13:15:59 +0000
parents e614dcabd870
children
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4
b6d9ea2fb41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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1 <tool id="obi_sort" name="obisort" version="@TOOL_VERSION@" profile="@PROFILE@">
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2 <description>sorts sequence records according to the value of a given attribute</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="bio_tools"/>
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7 <expand macro="requirements"/>
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8 <expand macro="stdio"/>
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9
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10 <command><![CDATA[
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11 @GUNZIP_INPUT@
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12 obisort
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13 --without-progress-bar
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14 #if $key:
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15 -k '$key'
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16 #end if
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17 ${reverse}
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18 @INPUT_FORMAT@
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19 @OUT_FORMAT@
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20 input
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21 @GZIP_OUTPUT@
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22 > '$output'
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23 @GENERATE_GALAXY_JSON@
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24 ]]></command>
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25 <inputs>
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26 <param name="input" type="data" format="@INPUT_FORMATS@,txt,tabular" label="Input sequences file"/>
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27 <param
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28 name="key"
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29 type="text"
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30 label="Key"
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31 help="This key must be encoded in your FASTA/FASTQ headers as key=value. See help (below) for more information."
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32 optional="false"/>
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33 <param name="reverse" type="boolean" checked="false" truevalue="-r" falsevalue="" label="Sort in reverse order?" />
b6d9ea2fb41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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34 <expand macro="input_format_options_macro"/>
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35 <expand macro="out_format_macro"/>
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36 </inputs>
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37 <outputs>
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38 <data format="auto" name="output"/>
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39 </outputs>
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40 <tests>
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41 <test expect_num_outputs="1">
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42 <param name="input" value="output_obiclean_advanced.fasta" />
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43 <param name="key" value="count"/>
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44 <param name="reverse" value="False"/>
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45 <param name="out_format" value="fasta"/>
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46 <output name="output" file="output_obisort.fasta" ftype="fasta"/>
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47 </test>
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48 <test expect_num_outputs="1">
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49 <param name="input" value="output_obiclean_advanced.fasta" />
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50 <param name="key" value="count"/>
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51 <param name="reverse" value="True"/>
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52 <param name="out_format" value="fastq"/>
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53 <output name="output" file="output_obisort.fastq" ftype="fastqsanger"/>
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54 </test>
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55 </tests>
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56 <help><![CDATA[
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57
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58 .. class:: infomark
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59
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60 **What it does**
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61
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62 obisort sorts sequence records according to the value of a given attribute, which can be either numeric or alphanumeric.
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63
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64 @OBITOOLS_LINK@
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65
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66 **Inputs:**
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67
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68 For sorting by key, the input file must be in the
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69 `OBITools FASTA/FASTQ format <https://pythonhosted.org/OBITools/attributes.html>`_.
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70 If your file is an OBITools output, it should already be formatted correctly.
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71
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72 For FASTA files, your headers should look like this::
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73
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74 >my_sequence taxid=3456; direct=True; sample=A354; this is my pretty sequence
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75 ACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGT
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76 GTGCTGACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTGTTT
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77 AACGACGTTGCAGTACGTTGCAGT
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78
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79 Where ``taxid``, ``direct``, and ``sample`` are keys that can be used for sorting.
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80
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81 If your sequences don't have title, you can format the headers with a trailing semicolon like so::
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82
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83 >my_sequence key1=value1;
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84
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85 For sorting OBITools output files, a list of OBITools sequence attributes are documented
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86 `here <https://pythonhosted.org/OBITools/attributes.html#names-reserved-for-attributes>`_.
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87
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88 ]]>
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89 </help>
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90 <expand macro="citation" />
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91 </tool>