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annotate filter_fasta.xml @ 0:c1bd0c560018 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
author bebatut
date Tue, 02 Feb 2016 05:50:37 -0500
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c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
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1 <tool id="qiime_filter_fasta" name="filter fasta" version="1.9.1galaxy1">
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2 <description>This script can be applied to remove sequences from a fasta or
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3 fastq file based on input criteria.</description>
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4
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5 <macros>
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6 <import>macros.xml</import>
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7 </macros>
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8
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9 <expand macro="requirements" />
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10
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11 <command>
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12 <![CDATA[
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13 filter_fasta.py
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14 -f $input_fasta_fp
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15 -o $output_fasta_fp
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16 #if str($otu_map) != 'None':
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17 -m $otu_map
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18 #end if
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19
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20 #if str($seq_id_fp) != 'None':
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21 -s $seq_id_fp
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22 #end if
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23
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24 #if str($biom_fp) != 'None':
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25 -b $biom_fp
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26 #end if
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27
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28 #if str($subject_fasta_fp) != 'None':
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29 -a $subject_fasta_fp
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30 #end if
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31
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32 #if str($seq_id_prefix):
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33 -p $seq_id_prefix
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34 #end if
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35
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36 #if str($sample_id_fp) != 'None':
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37 --sample_id_fp=$sample_id_fp
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38 #end if
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39
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40 #if $negate:
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41 -n
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42 #end if
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43
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44 #if str($mapping_fp) != 'None':
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45 --mapping_fp=$mapping_fp
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46 #end if
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47
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48 #if str($valid_states):
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49 --valid_states=$valid_states
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50 #end if
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51 ]]>
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52 </command>
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53
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54 <inputs>
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55 <param label="-f/--input_fasta_fp: path to the input fasta file"
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56 name="input_fasta_fp" optional="False" type="data"/>
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57 <param label="-m/--otu_map: an OTU map where sequences ids are those
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58 which should be retained" name="otu_map" optional="True" type="data"/>
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59 <param label="-s/--seq_id_fp: A list of sequence identifiers (or tab-delimited
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60 lines with a seq identifier in the first field) which should be retained"
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61 name="seq_id_fp" optional="True" type="data"/>
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62 <param label="-b/--biom_fp: A biom file where otu identifiers should be
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63 retained" name="biom_fp" optional="True" type="data"/>
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64 <param label="-a/--subject_fasta_fp: A fasta file where the seq ids should
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65 be retained." name="subject_fasta_fp" optional="True" type="data"/>
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66 <param label="-p/--seq_id_prefix: keep seqs where seq_id starts with this
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67 prefix" name="seq_id_prefix" optional="True" type="text"/>
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68 <param label="--sample_id_fp: keep seqs where seq_id starts with a sample
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69 id listed in this file" name="sample_id_fp" optional="True"
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70 type="data"/>
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71 <param label="-n/--negate: discard passed seq ids rather than keep passed
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72 seq ids [default: False]" name="negate" selected="False"
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73 type="boolean"/>
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74 <param label="--mapping_fp: mapping file path (for use with --valid_states)
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75 [default: None]" name="mapping_fp" optional="True" type="data"/>
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76 <param label="--valid_states: description of sample ids to retain (for use
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77 with --mapping_fp) [default: None]" name="valid_states" optional="True"
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78 type="text"/>
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79 </inputs>
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80
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81 <outputs>
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82 <data format="txt" name="output_fasta_fp"/>
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83 </outputs>
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84
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85 <tests>
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86 <test>
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87 </test>
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88 </tests>
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89
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90 <help>
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91 <![CDATA[
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92
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93 **What it does**
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94
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95
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96 ]]>
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97 </help>
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98
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99 <citations>
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100 <expand macro="citations" />
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101 </citations>
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102 </tool>