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annotate fastx_clipper.xml @ 3:85263dc18cec draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
author iuc
date Tue, 08 May 2018 13:27:25 -0400
parents bdf1ce174e39
children 736b8f6ee456
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3
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1 <tool id="cshl_fastx_clipper" name="Clip" version="1.0.2">
2
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2 <description>adapter sequences</description>
3
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3 <macros>
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iuc
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4 <import>macros.xml</import>
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iuc
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5 </macros>
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iuc
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6 <expand macro="requirements" />
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iuc
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7 <command detect_errors="exit_code"><![CDATA[
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iuc
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8 @CATS@ fastx_clipper
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iuc
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9 -l $minlength
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iuc
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10 -a '$clip_source.clip_sequence'
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iuc
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11 -d $keepdelta
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iuc
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12 -o '$output'
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iuc
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13 -v
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14 $KEEP_N
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iuc
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15 $DISCARD_OPTIONS
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iuc
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16 @FQQUAL@
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17 ]]></command>
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18
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19 <inputs>
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20 <expand macro="fastx_input" />
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21
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iuc
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22 <param name="minlength" type="integer" value="15"
85263dc18cec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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23 label="Minimum sequence length (after clipping, sequences shorter than this length will be discarded" />
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24
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25 <conditional name="clip_source">
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26 <param name="clip_source_list" type="select" label="Source">
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27 <option value="prebuilt" selected="true">Standard (select from the list below)</option>
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28 <option value="user">Enter custom sequence</option>
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29 </param>
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30
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31 <when value="user">
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32 <param name="clip_sequence" label="Enter custom clipping sequence" type="text" value="AATTGGCC" />
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33 </when>
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34
2
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35 <when value="prebuilt">
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36 <param name="clip_sequence" type="select" label="Choose Adapter">
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37 <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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38 <column name="name" index="1"/>
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39 <column name="value" index="0"/>
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40 </options>
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41 </param>
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42 </when>
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43 </conditional>
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44
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iuc
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45 <param name="keepdelta" type="integer" value="0"
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iuc
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46 label="Enter a non-zero value to keep the adapter sequence and x bases that follow it"
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47 help="Use this for hairpin barcoding. keep at 0 unless you know what you're doing" />
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48
2
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49 <param name="KEEP_N" type="select" label="Discard sequences with unknown (N) bases">
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50 <option value="">Yes</option>
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51 <option value="-n">No</option>
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52 </param>
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53
2
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54 <param name="DISCARD_OPTIONS" type="select" label="Output options">
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55 <option value="-c">Output only clipped sequences (i.e. sequences which contained the adapter)</option>
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56 <option value="-C">Output only non-clipped sequences (i.e. sequences which did not contained the adapter)</option>
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57 <option value="">Output both clipped and non-clipped sequences</option>
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58 </param>
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59 </inputs>
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60 <outputs>
3
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61 <data name="output" format_source="input" metadata_source="input" />
2
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62 </outputs>
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63 <tests>
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64 <test>
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65 <param name="input" value="fastx_clipper1.fastq" ftype="fastqsolexa"/>
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66 <param name="maxmismatches" value="2" />
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67 <param name="minlength" value="15" />
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68 <param name="clip_source_list" value="user" />
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69 <param name="clip_sequence" value="CAATTGGTTAATCCCCCTATATA" />
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70 <param name="keepdelta" value="0" />
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71 <param name="KEEP_N" value="-n" />
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72 <param name="DISCARD_OPTIONS" value="-c" />
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73 <output name="output" ftype="fastqsolexa" file="fastx_clipper1a.out" />
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74 </test>
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75 </tests>
3
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76 <help><![CDATA[
0
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77 **What it does**
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78
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79 This tool clips adapters from the 3'-end of the sequences in a FASTA/FASTQ file.
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80
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81 --------
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82
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83
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84 **Clipping Illustration:**
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85
2
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86 .. image:: fastx_clipper_illustration.png
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87
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88 **Clipping Example:**
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89
2
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90 .. image:: fastx_clipper_example.png
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91
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92 **In the above example:**
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93
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94 * Sequence no. 1 was discarded since it wasn't clipped (i.e. didn't contain the adapter sequence). (**Output** parameter).
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95 * Sequence no. 5 was discarded --- it's length (after clipping) was shorter than 15 nt (**Minimum Sequence Length** parameter).
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96
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97 ------
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98
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99 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
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100
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101 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
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85263dc18cec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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102 ]]></help>
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103 <expand macro="citations" />
0
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104 </tool>