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annotate emboss_garnier.xml @ 20:21a9fb508031 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
author iuc
date Tue, 31 Aug 2021 08:05:39 +0000
parents 27c43fb015f0
children
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27c43fb015f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 9844cae766e7471d9fa6b2e8356e5194e77f6753
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1 <tool id="EMBOSS: garnier40" name="garnier" version="@VERSION@">
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2 <description>Predicts protein secondary structure</description>
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21a9fb508031 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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3 <expand macro="bio_tools" />
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4 <macros>
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5 <import>macros.xml</import>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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6 </macros>
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7 <expand macro="requirements" />
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8 <code file="emboss_format_corrector.py" />
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9 <command>garnier -sequence '$input1' -outfile '$out_file1' -idc $idc -rformat2 $out_format1 -auto</command>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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10 <inputs>
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11 <param name="input1" type="data" format="data" label="Sequences" />
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12 <param name="idc" type="select" label="idc" help="In their paper, GOR mention that if you know something about the secondary structure content of the protein you are analyzing, you can do better in prediction. 'idc' is an index into a set of arrays, dharr[] and dsarr[], which provide 'decision constants' (dch, dcs), which are offsets that are applied to the weights for the helix and sheet (extend) terms. So, idc=0 says don't use the decision constant offsets, and idc=1 to 6 indicates that various combinations of dch,dcs offsets should be used">
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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13 <option value="0">idc 0</option>
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14 <option value="1">idc 1</option>
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15 <option value="2">idc 2</option>
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16 <option value="3">idc 3</option>
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17 <option value="4">idc 4</option>
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18 <option value="5">idc 5</option>
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19 <option value="6">idc 6</option>
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20 </param>
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21 <param name="out_format1" type="select" label="Output report file format">
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22 <option value="tagseq">TagSeq</option>
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23 <option value="embl">EMBL</option>
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24 <option value="genbank">GENBANK</option>
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25 <option value="gff">GFF</option>
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26 <option value="pir">PIR</option>
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27 <option value="swiss">SwissProt</option>
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28 <option value="dbmotif">DbMotif</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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29 <option value="diffseq">Diffseq</option>
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30 <option value="excel">Excel (tab delimited)</option>
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31 <option value="feattable">FeatTable</option>
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32 <option value="motif">Motif</option>
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33 <option value="regions">Regions</option>
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34 <option value="seqtable">SeqTable</option>
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35 <option value="simple">SRS Simple</option>
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36 <option value="srs">SRS</option>
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37 <option value="table">Table</option>
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38 </param>
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39 </inputs>
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40 <outputs>
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41 <data name="out_file1" format="garnier" />
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42 </outputs>
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43 <tests>
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44 <test>
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45 <param name="input1" value="2.fasta"/>
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46 <param name="idc" value="0"/>
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47 <param name="out_format1" value="excel"/>
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48 <output name="out_file1" file="emboss_garnier_out.tabular"/>
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49 </test>
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50 </tests>
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51 <help>
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52 You can view the original documentation here_.
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53
11
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54 .. _here: https://galaxy-iuc.github.io/emboss-5.0-docs/garnier.html
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55 </help>
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56 <expand macro="citations" />
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57 </tool>