Mercurial > repos > padge > trimal
annotate trimal.xml @ 0:b15a3147e604 draft
"planemo upload for repository https://github.com/inab/trimal commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
author | padge |
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date | Fri, 25 Mar 2022 17:10:43 +0000 |
parents | |
children | 0d53577b962f |
rev | line source |
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0
b15a3147e604
"planemo upload for repository https://github.com/inab/trimal commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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1 <tool id="trimal" name="trimAl: a tool for automated alignment trimming" version="0.1.0" python_template_version="3.5"> |
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"planemo upload for repository https://github.com/inab/trimal commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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2 <requirements> |
b15a3147e604
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3 <requirement type="package" version="1.4.1">trimal</requirement> |
b15a3147e604
"planemo upload for repository https://github.com/inab/trimal commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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4 </requirements> |
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5 <command detect_errors="exit_code"><![CDATA[ |
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"planemo upload for repository https://github.com/inab/trimal commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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6 trimal -in $input1 -out $trimmed_output -htmlout $html_summary ${out_format_selector} |
b15a3147e604
"planemo upload for repository https://github.com/inab/trimal commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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7 #if $trimming_mode.mode_selector == "custom" |
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"planemo upload for repository https://github.com/inab/trimal commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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8 -gapthreshold $trimming_mode.gapthreshold |
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"planemo upload for repository https://github.com/inab/trimal commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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9 -simthreshold $trimming_mode.simthreshold |
b15a3147e604
"planemo upload for repository https://github.com/inab/trimal commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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10 -cons $trimming_mode.cons |
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11 #else: |
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12 $trimming_mode.mode_selector |
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13 #end if |
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14 ; |
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"planemo upload for repository https://github.com/inab/trimal commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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15 |
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"planemo upload for repository https://github.com/inab/trimal commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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16 ]]></command> |
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"planemo upload for repository https://github.com/inab/trimal commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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17 <inputs> |
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"planemo upload for repository https://github.com/inab/trimal commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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18 <param name="input1" type="data" format="fasta,clustal,pir,phylip,nexus" multiple="false" label="Alignment file (clustal, fasta, NBRF/PIR, nexus, phylip3.2, phylip)" optional="false" /> |
b15a3147e604
"planemo upload for repository https://github.com/inab/trimal commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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19 <conditional name="trimming_mode"> |
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"planemo upload for repository https://github.com/inab/trimal commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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20 <param name="mode_selector" type="select" label="Select trimming mode from the list"> |
b15a3147e604
"planemo upload for repository https://github.com/inab/trimal commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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21 <option value="-nogaps">nogaps. Remove all positions with gaps in the alignment.</option> |
b15a3147e604
"planemo upload for repository https://github.com/inab/trimal commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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22 <option value="-noallgaps">noallgaps. Remove columns composed only by gaps.</option> |
b15a3147e604
"planemo upload for repository https://github.com/inab/trimal commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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23 <option value="-gappyout">gappyout. Only uses information based on gaps' distribution. (see User Guide)</option> |
b15a3147e604
"planemo upload for repository https://github.com/inab/trimal commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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24 <option value="-strict">strict. (see User Guide)</option> |
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"planemo upload for repository https://github.com/inab/trimal commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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25 <option value="-strictplus">strictplus. (see User Guide)</option> |
b15a3147e604
"planemo upload for repository https://github.com/inab/trimal commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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26 <option value="custom">Custom mode</option> |
b15a3147e604
"planemo upload for repository https://github.com/inab/trimal commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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27 </param> |
b15a3147e604
"planemo upload for repository https://github.com/inab/trimal commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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28 <when value="custom"> |
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"planemo upload for repository https://github.com/inab/trimal commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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29 <param argument="-gapthreshold" type="float" optional="true" value="0.9" min="0.0" max="1.0" label="gap threshold" help="1 - (fraction of sequences with a gap allowed). Range: [0 - 1]" multiple="false"/> |
b15a3147e604
"planemo upload for repository https://github.com/inab/trimal commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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30 <param argument="-simthreshold" type="float" optional="true" value="0.9" min="0.0" max="1.0" label="similarity threshold" help="Minimum average similarity allowed. Range: [0 - 1]" multiple="false"/> |
b15a3147e604
"planemo upload for repository https://github.com/inab/trimal commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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31 <param argument="-cons" type="integer" optional="true" value="50" min="0" max="100" label="min conservance percentage" help="Minimum percentage of the positions in the original alignment to conserve." multiple="false"/> |
b15a3147e604
"planemo upload for repository https://github.com/inab/trimal commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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32 |
b15a3147e604
"planemo upload for repository https://github.com/inab/trimal commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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33 </when> |
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"planemo upload for repository https://github.com/inab/trimal commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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34 </conditional> |
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"planemo upload for repository https://github.com/inab/trimal commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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35 <param name="out_format_selector" type="select" label="Select trimmed alignment output format from the list"> |
b15a3147e604
"planemo upload for repository https://github.com/inab/trimal commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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36 <option value="-clustal">CLUSTAL format</option> |
b15a3147e604
"planemo upload for repository https://github.com/inab/trimal commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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37 <option value="-fasta">FASTA format</option> |
b15a3147e604
"planemo upload for repository https://github.com/inab/trimal commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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38 <option value="-fasta_m10">FASTA format. Sequences name length up to 10 characters.</option> |
b15a3147e604
"planemo upload for repository https://github.com/inab/trimal commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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39 <option value="-nbrf">NBRF/PIR format</option> |
b15a3147e604
"planemo upload for repository https://github.com/inab/trimal commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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40 <option value="-nexus">NEXUS format</option> |
b15a3147e604
"planemo upload for repository https://github.com/inab/trimal commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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41 <option value="-mega">MEGA format</option> |
b15a3147e604
"planemo upload for repository https://github.com/inab/trimal commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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42 <option value="-phylip">PHYLIP/PHYLIP4 format</option> |
b15a3147e604
"planemo upload for repository https://github.com/inab/trimal commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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43 <option value="-phylip_m10">PHYLIP/PHYLIP4 format. Sequences name length up to 10 characters</option> |
b15a3147e604
"planemo upload for repository https://github.com/inab/trimal commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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44 <option value="-phylip_paml">PHYLIP format compatible with PAML</option> |
b15a3147e604
"planemo upload for repository https://github.com/inab/trimal commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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45 <option value="-phylip_paml_m10">PHYLIP format compatible with PAML. Sequences name length up to 10 characters.</option> |
b15a3147e604
"planemo upload for repository https://github.com/inab/trimal commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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46 <option value="-phylip3.2">PHYLIP3.2 format</option> |
b15a3147e604
"planemo upload for repository https://github.com/inab/trimal commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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47 <option value="-phylip3.2_m10">PHYLIP3.2 format. Sequences name length up to 10 characters.</option> |
b15a3147e604
"planemo upload for repository https://github.com/inab/trimal commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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48 </param> |
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"planemo upload for repository https://github.com/inab/trimal commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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49 </inputs> |
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"planemo upload for repository https://github.com/inab/trimal commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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50 <outputs> |
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"planemo upload for repository https://github.com/inab/trimal commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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51 <data name="trimmed_output" format="fasta" label="Trimmed alignment."/> |
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"planemo upload for repository https://github.com/inab/trimal commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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52 <data name="html_summary" format="html" label="trimal html summary."/> |
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"planemo upload for repository https://github.com/inab/trimal commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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53 </outputs> |
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"planemo upload for repository https://github.com/inab/trimal commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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54 <tests> |
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"planemo upload for repository https://github.com/inab/trimal commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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55 <test> |
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56 <param name="input1" value="example.009.AA.fasta"/> |
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57 <param name="mode_selector" value="-gappyout" /> |
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"planemo upload for repository https://github.com/inab/trimal commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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58 <param name="out_format_selector" value="-mega" /> |
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"planemo upload for repository https://github.com/inab/trimal commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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59 <output name="trimmed_output" file="trimmed_example.009.AA.mega" lines_diff="2"/> |
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"planemo upload for repository https://github.com/inab/trimal commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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60 <output name="html_summary" file="trimmed_example.009.AA.html"/> |
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"planemo upload for repository https://github.com/inab/trimal commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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61 </test> |
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62 <test> |
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63 <param name="input1" value="example.009.AA.fasta"/> |
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64 <param name="mode_selector" value="custom" /> |
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"planemo upload for repository https://github.com/inab/trimal commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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65 <param name="gapthreshold" value="0.5" /> |
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66 <param name="simthreshold" value="0.5" /> |
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67 <param name="cons" value="5" /> |
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68 <param name="out_format_selector" value="-phylip_paml_m10" /> |
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69 <output name="trimmed_output" file="custom_trimmed_example.009.AA.phy" /> |
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70 <output name="html_summary" file="custom_trimmed_example.009.AA.html"/> |
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71 </test> |
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72 </tests> |
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73 <help><![CDATA[ |
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74 Modes |
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75 -nogaps Remove all positions with gaps in the alignment. |
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76 -noallgaps Remove columns composed only by gaps. |
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77 -gappyout Use automatic selection on "gappyout" mode. This method only uses information based on gaps' distribution. (see User Guide). |
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78 -strict Use automatic selection on "strict" mode. (see User Guide). |
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79 -strictplus Use automatic selection on "strictplus" mode. (see User Guide). |
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80 trimAl v1.4.rev15 build[2013-12-17]. 2009-2013. Salvador Capella-Gutierrez and Toni Gabaldón. |
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81 |
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82 Custom mode parameters |
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83 -gt -gapthreshold <n> 1 - (fraction of sequences with a gap allowed). |
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84 -st -simthreshold <n> Minimum average similarity allowed. |
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85 -cons <n> Minimum percentage of the positions in the original alignment to conserve. |
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86 |
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87 Output formats |
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88 -nbrf Output file in NBRF/PIR format |
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89 -mega Output file in MEGA format |
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90 -nexus Output file in NEXUS format |
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91 -clustal Output file in CLUSTAL format |
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92 -fasta Output file in FASTA format |
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93 -fasta_m10 Output file in FASTA format. Sequences name length up to 10 characters. |
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94 -phylip Output file in PHYLIP/PHYLIP4 format |
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95 -phylip_m10 Output file in PHYLIP/PHYLIP4 format. Sequences name length up to 10 characters. |
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96 -phylip_paml Output file in PHYLIP format compatible with PAML |
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97 -phylip_paml_m10 Output file in PHYLIP format compatible with PAML. Sequences name length up to 10 characters. |
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98 -phylip3.2 Output file in PHYLIP3.2 format |
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99 -phylip3.2_m10 Output file in PHYLIP3.2 format. Sequences name length up to 10 characters. |
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100 |
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101 trimAl webpage: http://trimal.cgenomics.org |
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102 |
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103 This program is free software: you can redistribute it and/or modify |
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104 it under the terms of the GNU General Public License as published by |
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105 the Free Software Foundation, the last available version. |
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106 |
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107 Please cite: |
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108 trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. |
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109 Salvador Capella-Gutierrez; Jose M. Silla-Martinez; Toni Gabaldon. |
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110 Bioinformatics 2009, 25:1972-1973. |
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111 ]]></help> |
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112 <citations> |
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113 <citation type="bibtex"> |
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114 @misc{githubTrimAl, |
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115 author = {LastTODO, FirstTODO}, |
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116 year = {TODO}, |
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117 title = {TrimAl}, |
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118 publisher = {GitHub}, |
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119 journal = {GitHub repository}, |
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120 url = {https://github.com/inab/trimal}, |
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121 }</citation> |
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122 </citations> |
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123 </tool> |