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annotate align_seqs.xml @ 0:c1bd0c560018 draft default tip

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author bebatut
date Tue, 02 Feb 2016 05:50:37 -0500
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1 <tool id="qiime_align_seqs" name="Align sequences" version="1.9.1">
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2 <description>using a variety of alignment methods</description>
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3
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7
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8 <expand macro="requirements" />
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9
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10 <version_command><![CDATA[
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11 align_seqs.py --version
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12 ]]>
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13 </version_command>
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14
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15 <command>
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16 <![CDATA[
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17 align_seqs.py
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18 -i $input_fasta_fp
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19 -o align_seqs
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20 -m $alignment.alignment_method
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21
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22 #if $alignment.alignment_method == 'pynast':
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23 -a $alignment.pairwise_alignment_method
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24 #end if
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25
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26 #if str($template_fp) != 'None':
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27 -t $template_fp
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28 #end if
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29
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30 #if $min_length:
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31 -e $min_length
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32 #end if
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33
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34 -p $min_percent_id
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35 ]]>
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36 </command>
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37
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38 <inputs>
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39 <param name="input_fasta_fp" type="data" format="fasta"
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40 label="Input fasta file" help="(-i/--input_fasta_fp)"/>
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41
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42 <conditional name="alignment">
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43 <param name="alignment_method" type="select"
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44 label="Method for aligning sequences" help="(-m/--alignment_method)">
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45 <option value="pynast" selected="True" >pynast</option>
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46 <option value="infernal" >infernal</option>
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47 <option value="clustalw" >clustalw</option>
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48 <option value="muscle" >muscle</option>
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49 <option value="mafft" >mafft</option>
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50 </param>
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51 <when value="pynast">
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52 <param name="pairwise_alignment_method" type="select"
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53 label="Method for performing pairwise alignment in PyNAST"
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54 help="(-a/--pairwise_alignment_method)">
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55 <option value="muscle" >muscle</option>
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56 <option value="pair_hmm" >pair_hmm</option>
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57 <option value="clustal" >clustal</option>
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58 <option value="blast" >blast</option>
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59 <option value="uclust" selected="True" >uclust</option>
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60 <option value="mafft" >mafft</option>
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61 </param>
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62 </when>
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63 <when value="infernal" />
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64 <when value="clustalw" />
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65 <when value="muscle" />
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66 <when value="mafft" />
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67 </conditional>
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68
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69 <param name="template_fp" type="data" format="fasta"
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70 label="Fasta file for template alignment" help="(-t/--template_fp)"
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71 optional="True"/>
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72
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73 <param name="min_length" type="integer" label="Minimum sequence
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74 length to include in alignment" help="By default, 75% of the median
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75 input sequence length (-e/--min_length)" optional="True"/>
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76
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77 <param name="min_percent_id" type="float" value="0.75" label="Minimum
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78 percent sequence identity to closest blast hit to include sequence
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79 in alignment" help="(-p/--min_percent_id)"/>
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80 </inputs>
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81
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82 <outputs>
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83 <data name="aligned_sequences" format="fasta"
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84 from_work_dir="align_seqs/*_aligned.fasta"
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85 label="${tool.name} on ${on_string}: Aligned sequences" />
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86
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87 <data name="failures_sequences" format="fasta"
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88 from_work_dir="align_seqs/*_failures.fasta"
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89 label="${tool.name} on ${on_string}: Failure sequences">
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90 <filter> alignment['alignment_method'] == 'pynast'</filter>
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91 </data>
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92
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93 <data name="log" format="txt" from_work_dir="align_seqs/*_log.txt"
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94 label="${tool.name} on ${on_string}: Log"/>
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95 </outputs>
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96
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97 <tests>
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98 <test>
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99 <param name="input_fasta_fp" value=""/>
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100 <param name="alignment_method" value="pynast"/>
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101 <param name="pairwise_alignment_method" value="muscle"/>
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102 <param name="min_percent_id" value="0.75" />
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103 <output name="aligned_sequences"
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104 value="align_seqs_aligned_sequences.fasta"/>
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105 <output name="failures_sequences"
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106 value="align_seqs_failures_sequences.fasta"/>
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107 <output name="log" value="align_seqs_log.txt"/>
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108 </test>
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109 </tests>
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110
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111 <help><![CDATA[
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112
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113 **What it does?**
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114
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115 This tool aligns the sequences in a FASTA file to each other or to a template sequence alignment, depending on the method chosen.
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116
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117 More information about this tool is available on
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118 `QIIME documentation <http://qiime.org/scripts/align_seqs.html>`_.
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119 ]]>
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120 </help>
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121
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122 <citations>
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123 <expand macro="citations" />
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124 <citation type="doi">10.1093/bioinformatics/btp636</citation>
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125 <citation type="doi">10.1093/nar/gkh340</citation>
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126 <citation type="doi">10.1093/bioinformatics/btp157</citation>
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127 </citations>
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128 </tool>