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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mergegffs commit 230f5fe14cc469e56626201a5c377686976d81fc-dirty
author eduardo
date Mon, 26 Jun 2017 03:49:04 -0400
parents 8d0c12c9241d
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1 <tool id="mergegff" name="Merge gff using gffutils" version="1.0">
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2 <requirements>
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3 <requirement type="package" version="0.8">gffutils</requirement>
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4 <requirement type="package" version="1.0">genomegtftools</requirement>
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5 <requirement type="package" version="1.66">biopython</requirement>
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6 </requirements>
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7 <stdio>
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8 <exit_code range="1:" />
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9 </stdio>
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10 <version_command>
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11 <![CDATA[
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12 MergeGFF version 1.0
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13 ]]>
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14 </version_command>
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15 <command><![CDATA[
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17
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18 python $__tool_directory__/mergegffs.py -p $gff -d $sqlitedb -o $output
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19 #if $blastp:
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20 -b '$blastp'
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21 #end if
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22 #if $blastx:
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23 -x '$blastx'
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24 #end if
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25 #if $hmmscan:
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26 -f '$hmmscan'
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27 #end if
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28 #if $tmhmm:
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29 -t '$tmhmm'
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30 #end if
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31 #if $signalp:
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32 -s '$signalp'
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33 #end if
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34
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35
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36 ]]></command>
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37 <inputs>
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38 <!--
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39 <param name="transcriptome" type="data" format="fasta" optional="false" label="Transcripts" help="Assembled Transcripts fasta" />
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40 <param name="peptides" type="data" format="fasta" optional="false" label="Peptide predictions" help="Predicted peptides in fasta format" />
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41 <param name="gene_trans_map" type="data" format="tabular" optional="false" label="Genes to transcripts map" help="Genes to transcripts map output. Containing correspondance between gene ids and transcript ids either generated by Trinity of generated with a clustering algorithm " />
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42 -->
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43 <param name="gff" type="data" format="gff" optional="false" label="Peptides coordinates" help="Peptides prediction coordinates in gff format " />
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44
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45 <param name="blastp" type="data" format="tabular" optional="true" label="BLASTP: Peptides vs related species" help="[optional] NCBI BLAST+ blastp output. Output format: XML" />
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46 <param name="blastx" type="data" format="tabular" optional="true" label="BLASTX: Transcripts vs related species" help="[optional] NCBI BLAST+ blastx output. Output format: XML" />
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47 <param name="hmmscan" type="data" format="txt" optional="true" label="HMMER hmmscan: Peptides vs PFAM" help="[optional] HMMER hmmscan output: Table of per-domain hits. Output format: Table of per-domain hits (--domtblout)" />
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48 <param name="tmhmm" type="data" format="tabular" optional="true" label="TMHMM on Peptides" help="[optional]"/>
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49 <param name="signalp" type="data" format="tabular" optional="true" label="SignalP on Peptides" help="[optional]" />
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50 <!--
0
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51 <conditional name="cond_modify">
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52 <param name="select_existing" type="select" label="Use an existing gffutils db from history">
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53 <option value="yes" >Yes</option>
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54 <option value="no" selected="True">No</option>
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55 </param>
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56 <when value="yes">
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57 <param name="gffutils_sqlite_in" type="data" format="sqlite" optional="false" label="Existing GFFUtils SQLite database" help="http://daler.github.io/gffutils/index.html" />
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58 </when>
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59 <when value="no" />
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60 </conditional>
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61 -->
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62 <section name="filter_option" title="Filter options" expanded="False">
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63 <param argument="-E" type="float" value="1e-5" label="Maximum E-value for reporting best blast hit and associated annotations." />
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64
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65 </section>
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66 <param name="keep_sqlite" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Keep the sqlite database file" help="Can be used for visualization purpose" />
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67 </inputs>
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68 <outputs>
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69 <data name="output" format="tabular" label="Merged gff" >
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70 </data>
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71 <data name="sqlitedb" format="sqlite" label="Gffutils sqlite database" >
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72 <filter>keep_sqlite</filter>
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73 </data>
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74 </outputs>
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75 <tests>
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76 <test>
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77 <param name="gff" value="Trinity.fasta.transdecoder.gff3" />
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78 <param name="blastp" value="swissprot.blastp.outfmt6" />
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79 <param name="blastx" value="swissprot.blastx.outfmt6" />
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80 <param name="hmmscan" value="TrinotatePFAM.out" />
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81 <param name="tmhmm" value="tmhmm.out" />
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82 <param name="signalp" value="signalp.out" />
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83 <param name="keep_sqlite" value="false" />
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84 <output name="output" file="output.gff" />
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85 </test>
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86
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87 </tests>
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88 <help><![CDATA[
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89 .. class:: infomark
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90
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91 **What it does**
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92
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93 This tool loads annotations from multiple tools into a gffutils sqlite database and outputs a single gff file containing all annotations.
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94 The sqlite db can be used for filtering and visualization.
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95
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96 Based on https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate
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97
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98
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99 --------
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100
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101 **Suggested upstream Galaxy tools**
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102
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103 Transcripts
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104
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105 - Trinity: iuc/trinity_
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106
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107 .. _trinity: https://toolshed.g2.bx.psu.edu/repository?repository_id=faf6028922d9220a
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108
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109 Peptides
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110
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111 - TransDecoder: iuc/transdecoder_
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112
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113 .. _transdecoder: https://toolshed.g2.bx.psu.edu/repository?repository_id=7a2a8151a50f8099
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114
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115 Genes to transcripts map
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116
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117 - Generate gene to transcript map for Trinity assembly: iuc/trinity_gene_to_trans_map_
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118
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119 .. _trinity_gene_to_trans_map: https://toolshed.g2.bx.psu.edu/repository?repository_id=faf6028922d9220a
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120
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121 BLASTP: Peptides vs Uniprot.SwissProt
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122
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123 - NCBI BLAST+ blastp: devteam/ncbi_blast_plus_
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124
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125 .. _ncbi_blast_plus: https://toolshed.g2.bx.psu.edu/repository?repository_id=1d92ebdf7e8d466c
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126
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127 BLASTX: Transcripts vs Uniprot.SwissProt
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128
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129 - NCBI BLAST+ blastx: devteam/ncbi_blast_plus_
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130
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131 .. _ncbi_blast_plus: https://toolshed.g2.bx.psu.edu/repository?repository_id=1d92ebdf7e8d466c
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132
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133 HMMER hmmscan: Peptides vs PFAM
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134
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135 - HMMER hmmscan: iuc/hmmer_hmmscan_
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136
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137 .. _hmmer_hmmscan: https://toolshed.g2.bx.psu.edu/repository?repository_id=a2cc4683090b1800
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138
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139 TMHMM on Peptides
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140
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141 - TMHMM 2.0: peterjc/tmhmm_and_signalp_
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142
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143 .. _tmhmm_and_signalp: https://toolshed.g2.bx.psu.edu/repository?repository_id=292389a45f1a238a
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144
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145 SignalP on Peptides
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146
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147 - SignalP 3.0: peterjc/tmhmm_and_signalp_
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148
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149 .. _tmhmm_and_signalp: https://toolshed.g2.bx.psu.edu/repository?repository_id=292389a45f1a238a
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150
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151
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152
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153
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154 --------
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155
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156
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157 ]]></help>
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158 <citations>
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159
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160 </citations>
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161 </tool>