Mercurial > repos > damion > ffp_phylogeny
comparison ffp_phylogeny.xml @ 1:d1c88b118a3f draft
Uploaded
| author | damion |
|---|---|
| date | Fri, 13 Mar 2015 20:59:28 -0400 |
| parents | eb6e5e78a066 |
| children | 671667722d3d |
comparison
equal
deleted
inserted
replaced
| 0:eb6e5e78a066 | 1:d1c88b118a3f |
|---|---|
| 1 <tool id="ffp_phylogeny" name="Feature Frequency Profile Phylogeny" version="0.1.00"> | 1 <tool id="ffp_phylogeny" name="Feature Frequency Profile Phylogeny" version="0.1.02"> |
| 2 <description>An alignment free comparison tool for phylogenetic analysis and text comparison</description> | 2 <description>An alignment free comparison tool for phylogenetic analysis and text comparison</description> |
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="package" version="0.3.19_d4382db015acec0e5cc43d6c1ac80ae12cb7e6b3">ffp-phylogeny</requirement> | 4 <requirement type="package" version="0.3.19_d4382db015acec0e5cc43d6c1ac80ae12cb7e6b3">ffp-phylogeny</requirement> |
| 5 </requirements> | 5 </requirements> |
| 6 | 6 |
| 20 #end for | 20 #end for |
| 21 " | 21 " |
| 22 -t "$(sequence.file_type.split('-')[0])" | 22 -t "$(sequence.file_type.split('-')[0])" |
| 23 -l "$length" | 23 -l "$length" |
| 24 -o "$info" | 24 -o "$info" |
| 25 ##if $normalize: | 25 ##if $normalize |
| 26 ## -n | 26 ## -n |
| 27 ##end if | 27 ##end if |
| 28 #if $sequence.file_type != 'text': | 28 #if $sequence.file_type != 'text' |
| 29 #if $sequence.file_type.find('multi') > 0: | 29 #if $sequence.file_type == 'amino-multi' or $sequence.file_type == 'nucleotide-multi' |
| 30 -m | 30 -m |
| 31 #end if | 31 #end if |
| 32 #if $sequence.grouping: | 32 #if $sequence.groupings |
| 33 #pass | |
| 34 #else | |
| 33 -d | 35 -d |
| 34 #end if | 36 #end if |
| 35 #if $metric: | 37 #if $metric |
| 36 -M "$metric" | 38 -M "$metric" |
| 37 #end if | 39 #end if |
| 38 #if $similarity: | 40 #if $similarity |
| 39 -s | 41 -s |
| 40 #end if | 42 #end if |
| 41 #if $abbreviate: | 43 #if $abbreviate |
| 42 -a | 44 -a |
| 43 #end if | 45 #end if |
| 44 #end if | 46 #end if |
| 45 #if $phylogeny.phylo_type == 'filter': | 47 #if $phylogeny.phylo_type == 'filter' |
| 46 -f "$phylogeny.filt.filter_type" | 48 -f "$phylogeny.filt.filter_type" |
| 47 -L "$phylogeny.filt.lower" | 49 -L "$phylogeny.filt.lower" |
| 48 -U "$phylogeny.filt.upper" | 50 -U "$phylogeny.filt.upper" |
| 49 #end if | 51 #end if |
| 50 #if $tree: | 52 #if $tree |
| 51 -T | 53 -T |
| 52 #end if | 54 #end if |
| 53 | |
| 54 ##ffpjsd -n FLOAT , --normval=FLOAT | 55 ##ffpjsd -n FLOAT , --normval=FLOAT |
| 55 ## For option -e, --euclid, change the n-norm distance (Default is n=2) to any other value where n > 1 | 56 ## For option -e, --euclid, change the n-norm distance (Default is n=2) to any other value where n > 1 |
| 56 | 57 |
| 57 ]]></command> | 58 ]]></command> |
| 58 <expand macro="stdio" /> | 59 <expand macro="stdio" /> |
| 64 <param name="length" type="integer" min="1" max="25" label="l-mer length" value="6" help="String of valid characters of this length will be counted. Synonyms: feature, k-mer, n-gram, k-tuple" size="2"/> | 65 <param name="length" type="integer" min="1" max="25" label="l-mer length" value="6" help="String of valid characters of this length will be counted. Synonyms: feature, k-mer, n-gram, k-tuple" size="2"/> |
| 65 <!-- | 66 <!-- |
| 66 <param name="normalize" label="Normalize counts into relative frequency" type="boolean" checked="true" help="" /> | 67 <param name="normalize" label="Normalize counts into relative frequency" type="boolean" checked="true" help="" /> |
| 67 --> | 68 --> |
| 68 <conditional name="sequence"> | 69 <conditional name="sequence"> |
| 69 <param type="select" name="file_type" label="File type" help="Note: For phylogeny display, at least three profiles are required, as files or fasta sequences within a file."> | 70 <param type="select" name="file_type" label="File type" help="Note: For phylogeny display, at least three profiles are required."> |
| 70 <option value="amino">Amino Acids, one sequence per file</option> | 71 <option value="amino">Amino Acids, one profile per file</option> |
| 71 <option value="amino-multi">Amino Acids, multiple fasta sequences per file</option> | 72 <option value="amino-multi">Amino Acids, one profile per fasta sequence in file</option> |
| 72 <option value="nucleotide">Nucleic acids, one sequence per file</option> | 73 <option value="nucleotide">Nucleic acids, one profile per file</option> |
| 73 <option value="nucleotide-multi">Nucleic acids, multiple fasta sequences per file</option> | 74 <option value="nucleotide-multi">Nucleic acids, one profile per fasta sequence in file</option> |
| 74 <option value="text">Text, single file</option> | 75 <option value="text">Text, single file</option> |
| 75 </param> | 76 </param> |
| 76 | 77 |
| 77 <when value="amino"><!-- ffpaa --> | 78 <when value="amino"><!-- ffpaa --> |
| 78 <param name="filesin" type="data" label="Select input file(s)" format="fasta" multiple="true" /> | 79 <param name="filesin" type="data" label="Select input file(s)" format="fasta" multiple="true" /> |
| 79 <param name="grouping" label="Enable amino acid grouping" type="boolean" checked="true" help="Counts amino acids in groups rather than individually (usually advantageous, see below)." /> | 80 <param name="groupings" label="Enable amino acid grouping" type="boolean" checked="true" help="Counts amino acids in groups rather than individually (usually advantageous, see below)." /> |
| 80 </when> | 81 </when> |
| 81 | 82 |
| 82 <when value="amino-multi"> | 83 <when value="amino-multi"> |
| 83 <param name="filesin" type="data" label="Select input file(s)" format="fasta" multiple="true" /> | 84 <param name="filesin" type="data" label="Select input file(s)" format="fasta" multiple="true" /> |
| 84 <param name="grouping" label="Enable amino acid grouping" type="boolean" checked="true" help="Counts amino acids in groups rather than individually (usually advantageous, see below)." /> | 85 <param name="groupings" label="Enable amino acid grouping" type="boolean" checked="true" help="Counts amino acids in groups rather than individually (usually advantageous, see below)." /> |
| 85 </when> | 86 </when> |
| 86 | 87 |
| 87 <when value="nucleotide"><!-- ffpry --> | 88 <when value="nucleotide"><!-- ffpry --> |
| 88 <param name="filesin" type="data" label="Select input file(s)" format="fasta" multiple="true" /> | 89 <param name="filesin" type="data" label="Select input file(s)" format="fasta" multiple="true" /> |
| 89 <param name="grouping" label="Enable purine / pyrimidine grouping" type="boolean" checked="true" help="Counts each nucleotide as a purine(R) or pyrimidine(Y) rather than individually (usually advantageous)." /> | 90 <param name="groupings" label="Enable purine / pyrimidine grouping" type="boolean" checked="true" help="Counts each nucleotide as a purine(R) or pyrimidine(Y) rather than individually (usually advantageous)." /> |
| 90 </when> | 91 </when> |
| 91 | 92 |
| 92 <when value="nucleotide-multi"> | 93 <when value="nucleotide-multi"> |
| 93 <param name="filesin" type="data" label="Select input file(s)" format="fasta" multiple="true" /> | 94 <param name="filesin" type="data" label="Select input file(s)" format="fasta" multiple="true" /> |
| 94 <param name="grouping" label="Enable purine / pyrimidine grouping" type="boolean" checked="true" help="Counts each nucleotide as a purine(R) or pyrimidine(Y) rather than individually (usually advantageous)." /> | 95 <param name="groupings" label="Enable purine / pyrimidine grouping" type="boolean" checked="true" help="Counts each nucleotide as a purine(R) or pyrimidine(Y) rather than individually (usually advantageous)." /> |
| 95 </when> | 96 </when> |
| 96 | 97 |
| 97 <when value="text"><!-- ffptxt --> | 98 <when value="text"><!-- ffptxt --> |
| 98 <param name="filesin" type="data" multiple="true"/> | 99 <param name="filesin" type="data" multiple="true"/> |
| 99 </when> | 100 </when> |
| 198 | 199 |
| 199 <tests> | 200 <tests> |
| 200 <test> | 201 <test> |
| 201 <param name="length" value="1"/> | 202 <param name="length" value="1"/> |
| 202 <param name="tree" value="0"/> | 203 <param name="tree" value="0"/> |
| 203 <param name="grouping" value="true"/> | 204 <param name="groupings" value="false"/> |
| 204 <param name="file_type" value="nucleotide"/> | 205 <param name="file_type" value="nucleotide"/> |
| 205 <param name="filesin" value="genome1,genome2"/> | 206 <param name="filesin" value="genome1,genome2"/> |
| 206 <output name="info" file="test_length_1_output.tabular"/> | 207 <output name="info" file="test_length_1_output.tabular"/> |
| 207 </test> | 208 </test> |
| 208 <test> | 209 <test> |
| 209 <param name="length" value="2"/> | 210 <param name="length" value="2"/> |
| 210 <param name="tree" value="0"/> | 211 <param name="tree" value="0"/> |
| 211 <param name="grouping" value="true"/> | 212 <param name="groupings" value="false"/> |
| 212 <param name="file_type" value="nucleotide"/> | 213 <param name="file_type" value="nucleotide"/> |
| 213 <param name="filesin" value="genome1,genome2"/> | 214 <param name="filesin" value="genome1,genome2"/> |
| 214 <output name="info" file="test_length_2_output.tabular"/> | 215 <output name="info" file="test_length_2_output.tabular"/> |
| 215 </test> | 216 </test> |
| 217 <test> | |
| 218 <param name="length" value="2"/> | |
| 219 <param name="tree" value="0"/> | |
| 220 <param name="groupings" value="true"/> | |
| 221 <param name="file_type" value="nucleotide-multi"/> | |
| 222 <param name="filesin" value="genome1,genome2"/> | |
| 223 <output name="info" file="test_length_2b_output.tabular"/> | |
| 224 </test> | |
| 216 </tests> | 225 </tests> |
| 217 | 226 |
| 218 <help><![CDATA[ | 227 <help><![CDATA[ |
| 219 | 228 |
| 220 .. class:: infomark | 229 .. class:: infomark |
| 222 | 231 |
| 223 **What it does** | 232 **What it does** |
| 224 | 233 |
| 225 FFP (Feature frequency profile) is an alignment free comparison tool for phylogenetic analysis and text comparison. It can be applied to nucleotide sequences, complete genomes, proteomes and even used for text comparison. | 234 FFP (Feature frequency profile) is an alignment free comparison tool for phylogenetic analysis and text comparison. It can be applied to nucleotide sequences, complete genomes, proteomes and even used for text comparison. |
| 226 | 235 |
| 227 This galaxy tool prepares a mini-pipeline consisting of **[ffpry | ffpaa | ffptxt] > [ ffpfilt | ffpcol > ffprwn] > ffpjsd > ffptree** . The last step is optional - by deselecting the "Generate Tree Phylogeny" checkbox, the tool will output a distance matrix rather than a Newick (.nhx) formatted tree file. | 236 This galaxy tool prepares a mini-pipeline consisting of **[ffpry | ffpaa | ffptxt] > [ ffpfilt | ffpcol > ffprwn] > ffpjsd > ffptree** . The last step is optional - by deselecting the "Generate Tree Phylogeny" checkbox, the tool will output only the precursor distance matrix file rather than a Newick (.nhx) formatted tree file. |
| 228 | 237 |
| 229 Each sequence or text file has a profile containing tallies of each feature found. A feature is a string of valid characters of given length. | 238 Each sequence or text file has a profile containing tallies of each feature found. A feature is a string of valid characters of given length. |
| 230 | 239 |
| 231 For nucleotide data, by default each character (ATGC) is grouped as either purine(R) or pyrmidine(Y) before being counted. | 240 For nucleotide data, by default each character (ATGC) is grouped as either purine(R) or pyrmidine(Y) before being counted. |
| 232 | 241 |