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annotate fastx_trimmer.xml @ 4:b98f3fa516a3 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer commit f3f313cb59922b945ac9587ff718b231d0f8db5c
author iuc
date Fri, 17 Aug 2018 05:06:06 -0400
parents bbb007a39ac2
children 547e8d00f11c
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4
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1 <tool id="cshl_fastx_trimmer" version="1.0.2" name="Trim sequences">
2
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2 <description></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_trimmer -v
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9 -f $first
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10 -l $last
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11 -o '$output'
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12 @FQQUAL@
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b98f3fa516a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer commit f3f313cb59922b945ac9587ff718b231d0f8db5c
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13
b98f3fa516a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer commit f3f313cb59922b945ac9587ff718b231d0f8db5c
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14 #if $input.is_of_type('fasta.gz', 'fastqsanger.gz', 'fastqsolexa.gz', 'fastqillumina.gz'):
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15 -z
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16 #end if
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17
3
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18 ]]></command>
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19 <inputs>
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20 <expand macro="fastx_input" />
bbb007a39ac2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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21 <param name="first" type="integer" value="1" label="First base to keep" />
bbb007a39ac2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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22 <param name="last" type="integer" value="21" label="Last base to keep" />
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23 </inputs>
377ac2829eac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_trimmer commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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24 <outputs>
3
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25 <data name="output" format_source="input" metadata_source="input" />
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26 </outputs>
377ac2829eac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_trimmer commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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27 <tests>
377ac2829eac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_trimmer commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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28 <test>
377ac2829eac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_trimmer commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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29 <!-- Trim a FASTA file - remove first four bases (e.g. a barcode) -->
377ac2829eac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_trimmer commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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30 <param name="input" value="fastx_trimmer1.fasta" />
377ac2829eac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_trimmer commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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31 <param name="first" value="5"/>
377ac2829eac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_trimmer commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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32 <param name="last" value="36"/>
377ac2829eac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_trimmer commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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33 <output name="output" ftype="fasta" file="fastx_trimmer1.out" />
377ac2829eac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_trimmer commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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34 </test>
377ac2829eac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_trimmer commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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35 <test>
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36 <!-- Trim a FASTQ file - remove last 9 bases (e.g. keep only miRNA length sequences) -->
377ac2829eac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_trimmer commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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37 <param name="input" value="fastx_trimmer2.fastq" ftype="fastqsolexa"/>
377ac2829eac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_trimmer commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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38 <param name="first" value="1"/>
377ac2829eac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_trimmer commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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39 <param name="last" value="27"/>
377ac2829eac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_trimmer commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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40 <output name="output" ftype="fastqsolexa" file="fastx_trimmer2.out" />
377ac2829eac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_trimmer commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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41 </test>
4
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42 <test>
b98f3fa516a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer commit f3f313cb59922b945ac9587ff718b231d0f8db5c
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43 <!-- Trim a FASTQ.gz file and output FASTQ.gz -->
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44 <param name="input" value="fastx_trimmer2.fastq.gz" ftype="fastqsanger.gz"/>
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45 <param name="first" value="1"/>
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46 <param name="last" value="27"/>
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47 <output name="output" ftype="fastqsanger.gz" decompress="true" file="fastx_trimmer2.out.gz" />
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48 </test>
2
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49 </tests>
3
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50 <help><![CDATA[
0
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51 **What it does**
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52
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53 This tool trims (cut bases from) sequences in a FASTA/Q file.
2
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54
0
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55 --------
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56
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57 **Example**
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58
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59 Input Fasta file (with 36 bases in each sequences)::
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60
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61 >1-1
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62 TATGGTCAGAAACCATATGCAGAGCCTGTAGGCACC
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63 >2-1
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64 CAGCGAGGCTTTAATGCCATTTGGCTGTAGGCACCA
2
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65
0
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66 Trimming with First=1 and Last=21, we get a FASTA file with 21 bases in each sequences (starting from the first base)::
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67
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68 >1-1
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69 TATGGTCAGAAACCATATGCA
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70 >2-1
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71 CAGCGAGGCTTTAATGCCATT
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72
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73 Trimming with First=6 and Last=10, will generate a FASTA file with 5 bases (bases 6,7,8,9,10) in each sequences::
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74
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75 >1-1
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76 TCAGA
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77 >2-1
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78 AGGCT
2
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79
0
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80 ------
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81
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82 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
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83
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84 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
3
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85 ]]></help>
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86 <expand macro="citations" />
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87 <!-- FASTX-Trimmer is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
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88 </tool>