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annotate fastx_clipper.xml @ 4:397201fefb9e draft

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author iuc
date Wed, 22 Aug 2018 11:03:05 -0400
parents 410c5d0b638a
children 40200bfa25cd
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4
397201fefb9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit 3953b65f6b1c0336e9cadbe0792a5d3b14b5643a
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1 <tool id="cshl_fastx_clipper" name="Clip" version="1.0.3">
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>
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6 <expand macro="requirements" />
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7 <command detect_errors="exit_code"><![CDATA[
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8 @CATS@ fastx_clipper
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9 -l $minlength
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10 -a '$clip_source.clip_sequence'
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11 -d $keepdelta
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12 -o '$output'
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13 -v
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14 $KEEP_N
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15 $DISCARD_OPTIONS
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16 @FQQUAL@
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17 @GZIP@
3
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18 ]]></command>
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19
2
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20 <inputs>
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21 <expand macro="fastx_input" />
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22
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23 <param name="minlength" type="integer" value="15"
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24 label="Minimum sequence length (after clipping, sequences shorter than this length will be discarded" />
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25
2
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26 <conditional name="clip_source">
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27 <param name="clip_source_list" type="select" label="Source">
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28 <option value="prebuilt" selected="true">Standard (select from the list below)</option>
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29 <option value="user">Enter custom sequence</option>
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30 </param>
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31
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32 <when value="user">
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33 <param name="clip_sequence" label="Enter custom clipping sequence" type="text" value="AATTGGCC" />
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34 </when>
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35
2
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36 <when value="prebuilt">
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37 <param name="clip_sequence" type="select" label="Choose Adapter">
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38 <options from_file="fastx_clipper_sequences.txt">
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39 <column name="name" index="1"/>
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40 <column name="value" index="0"/>
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41 </options>
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42 </param>
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43 </when>
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44 </conditional>
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45
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46 <param name="keepdelta" type="integer" value="0"
410c5d0b638a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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47 label="Enter a non-zero value to keep the adapter sequence and x bases that follow it"
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48 help="Use this for hairpin barcoding. keep at 0 unless you know what you're doing" />
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49
2
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50 <param name="KEEP_N" type="select" label="Discard sequences with unknown (N) bases">
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51 <option value="">Yes</option>
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52 <option value="-n">No</option>
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53 </param>
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54
2
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55 <param name="DISCARD_OPTIONS" type="select" label="Output options">
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56 <option value="-c">Output only clipped sequences (i.e. sequences which contained the adapter)</option>
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57 <option value="-C">Output only non-clipped sequences (i.e. sequences which did not contained the adapter)</option>
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58 <option value="">Output both clipped and non-clipped sequences</option>
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59 </param>
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60 </inputs>
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61 <outputs>
3
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62 <data name="output" format_source="input" metadata_source="input" />
2
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63 </outputs>
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64 <tests>
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65 <test>
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66 <param name="input" value="fastx_clipper1.fastq" ftype="fastqsolexa"/>
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67 <param name="maxmismatches" value="2" />
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68 <param name="minlength" value="15" />
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69 <param name="clip_source_list" value="user" />
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70 <param name="clip_sequence" value="CAATTGGTTAATCCCCCTATATA" />
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71 <param name="keepdelta" value="0" />
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72 <param name="KEEP_N" value="-n" />
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73 <param name="DISCARD_OPTIONS" value="-c" />
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74 <output name="output" ftype="fastqsolexa" file="fastx_clipper1a.out" />
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75 </test>
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76 </tests>
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77 <help><![CDATA[
0
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78 **What it does**
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79
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80 This tool clips adapters from the 3'-end of the sequences in a FASTA/FASTQ file.
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81
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82 --------
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83
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84
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85 **Clipping Illustration:**
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86
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87 .. image:: fastx_clipper_illustration.png
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88
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89 **Clipping Example:**
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90
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91 .. image:: fastx_clipper_example.png
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92
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93 **In the above example:**
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94
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95 * Sequence no. 1 was discarded since it wasn't clipped (i.e. didn't contain the adapter sequence). (**Output** parameter).
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96 * Sequence no. 5 was discarded --- it's length (after clipping) was shorter than 15 nt (**Minimum Sequence Length** parameter).
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97
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98 ------
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99
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100 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
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101
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102 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
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103 ]]></help>
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104 <expand macro="citations" />
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105 </tool>