Mercurial > repos > devteam > fastx_clipper

annotate fastx_clipper.xml @ 5:b8658f852bc7 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit 4c002e52261da2e7609735883d91fa1610ce6ce7"
author iuc
date Thu, 30 Jan 2020 13:30:10 -0500
parents 736b8f6ee456
children cb1e251cac37
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5
b8658f852bc7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit 4c002e52261da2e7609735883d91fa1610ce6ce7"
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1 <tool id="cshl_fastx_clipper" name="Clip" version="1.0.3+galaxy0">
2
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2 <description>adapter sequences</description>
3
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
5
b8658f852bc7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit 4c002e52261da2e7609735883d91fa1610ce6ce7"
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6 <expand macro="requirements">
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7 <requirement type="package" version="1.0.8">bzip2</requirement>
b8658f852bc7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit 4c002e52261da2e7609735883d91fa1610ce6ce7"
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8 </expand>
3
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9 <command detect_errors="exit_code"><![CDATA[
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10 @CATS@ fastx_clipper
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11 -l $minlength
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12 -a '$clip_source.clip_sequence'
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13 -d $keepdelta
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14 -v
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15 $KEEP_N
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16 $DISCARD_OPTIONS
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17 @FQQUAL@
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b8658f852bc7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit 4c002e52261da2e7609735883d91fa1610ce6ce7"
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18 @GZIP@ > '$output'
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19 ]]></command>
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21 <inputs>
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22 <expand macro="fastx_input" />
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23
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24 <param name="minlength" type="integer" value="15"
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25 label="Minimum sequence length (after clipping, sequences shorter than this length will be discarded" />
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26
2
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27 <conditional name="clip_source">
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28 <param name="clip_source_list" type="select" label="Source">
bdf1ce174e39 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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29 <option value="prebuilt" selected="true">Standard (select from the list below)</option>
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30 <option value="user">Enter custom sequence</option>
bdf1ce174e39 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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31 </param>
bdf1ce174e39 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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32
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33 <when value="user">
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34 <param name="clip_sequence" label="Enter custom clipping sequence" type="text" value="AATTGGCC" />
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35 </when>
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36
2
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37 <when value="prebuilt">
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38 <param name="clip_sequence" type="select" label="Choose Adapter">
bdf1ce174e39 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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39 <options from_file="fastx_clipper_sequences.txt">
bdf1ce174e39 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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40 <column name="name" index="1"/>
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41 <column name="value" index="0"/>
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42 </options>
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43 </param>
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44 </when>
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45 </conditional>
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46
3
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47 <param name="keepdelta" type="integer" value="0"
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48 label="Enter a non-zero value to keep the adapter sequence and x bases that follow it"
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49 help="Use this for hairpin barcoding. keep at 0 unless you know what you're doing" />
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50
2
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51 <param name="KEEP_N" type="select" label="Discard sequences with unknown (N) bases">
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52 <option value="">Yes</option>
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53 <option value="-n">No</option>
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54 </param>
0
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55
2
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56 <param name="DISCARD_OPTIONS" type="select" label="Output options">
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57 <option value="-c">Output only clipped sequences (i.e. sequences which contained the adapter)</option>
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58 <option value="-C">Output only non-clipped sequences (i.e. sequences which did not contained the adapter)</option>
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59 <option value="">Output both clipped and non-clipped sequences</option>
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60 </param>
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61 </inputs>
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62 <outputs>
3
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63 <data name="output" format_source="input" metadata_source="input" />
2
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64 </outputs>
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65 <tests>
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66 <test>
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67 <param name="input" value="fastx_clipper1.fastq" ftype="fastqsolexa"/>
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68 <param name="maxmismatches" value="2" />
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69 <param name="minlength" value="15" />
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70 <param name="clip_source_list" value="user" />
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71 <param name="clip_sequence" value="CAATTGGTTAATCCCCCTATATA" />
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72 <param name="keepdelta" value="0" />
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73 <param name="KEEP_N" value="-n" />
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74 <param name="DISCARD_OPTIONS" value="-c" />
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75 <output name="output" ftype="fastqsolexa" file="fastx_clipper1a.out" />
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76 </test>
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77 </tests>
3
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78 <help><![CDATA[
0
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79 **What it does**
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80
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81 This tool clips adapters from the 3'-end of the sequences in a FASTA/FASTQ file.
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82
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83 --------
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84
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85
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86 **Clipping Illustration:**
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87
2
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88 .. image:: fastx_clipper_illustration.png
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89
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90 **Clipping Example:**
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91
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92 .. image:: fastx_clipper_example.png
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93
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94 **In the above example:**
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95
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96 * Sequence no. 1 was discarded since it wasn't clipped (i.e. didn't contain the adapter sequence). (**Output** parameter).
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97 * Sequence no. 5 was discarded --- it's length (after clipping) was shorter than 15 nt (**Minimum Sequence Length** parameter).
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98
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99 ------
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100
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101 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
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102
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103 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
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104 ]]></help>
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105 <expand macro="citations" />
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106 </tool>