Mercurial > repos > damion > ffp_phylogeny
diff ffp_phylogeny.xml @ 1:d1c88b118a3f draft
Uploaded
| author | damion |
|---|---|
| date | Fri, 13 Mar 2015 20:59:28 -0400 |
| parents | eb6e5e78a066 |
| children | 671667722d3d |
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--- a/ffp_phylogeny.xml Mon Feb 23 18:25:25 2015 -0500 +++ b/ffp_phylogeny.xml Fri Mar 13 20:59:28 2015 -0400 @@ -1,4 +1,4 @@ -<tool id="ffp_phylogeny" name="Feature Frequency Profile Phylogeny" version="0.1.00"> +<tool id="ffp_phylogeny" name="Feature Frequency Profile Phylogeny" version="0.1.02"> <description>An alignment free comparison tool for phylogenetic analysis and text comparison</description> <requirements> <requirement type="package" version="0.3.19_d4382db015acec0e5cc43d6c1ac80ae12cb7e6b3">ffp-phylogeny</requirement> @@ -22,35 +22,36 @@ -t "$(sequence.file_type.split('-')[0])" -l "$length" -o "$info" - ##if $normalize: + ##if $normalize ## -n ##end if - #if $sequence.file_type != 'text': - #if $sequence.file_type.find('multi') > 0: + #if $sequence.file_type != 'text' + #if $sequence.file_type == 'amino-multi' or $sequence.file_type == 'nucleotide-multi' -m #end if - #if $sequence.grouping: + #if $sequence.groupings + #pass + #else -d #end if - #if $metric: + #if $metric -M "$metric" #end if - #if $similarity: + #if $similarity -s #end if - #if $abbreviate: + #if $abbreviate -a #end if #end if - #if $phylogeny.phylo_type == 'filter': + #if $phylogeny.phylo_type == 'filter' -f "$phylogeny.filt.filter_type" -L "$phylogeny.filt.lower" -U "$phylogeny.filt.upper" #end if - #if $tree: + #if $tree -T #end if - ##ffpjsd -n FLOAT , --normval=FLOAT ## For option -e, --euclid, change the n-norm distance (Default is n=2) to any other value where n > 1 @@ -66,32 +67,32 @@ <param name="normalize" label="Normalize counts into relative frequency" type="boolean" checked="true" help="" /> --> <conditional name="sequence"> - <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."> - <option value="amino">Amino Acids, one sequence per file</option> - <option value="amino-multi">Amino Acids, multiple fasta sequences per file</option> - <option value="nucleotide">Nucleic acids, one sequence per file</option> - <option value="nucleotide-multi">Nucleic acids, multiple fasta sequences per file</option> + <param type="select" name="file_type" label="File type" help="Note: For phylogeny display, at least three profiles are required."> + <option value="amino">Amino Acids, one profile per file</option> + <option value="amino-multi">Amino Acids, one profile per fasta sequence in file</option> + <option value="nucleotide">Nucleic acids, one profile per file</option> + <option value="nucleotide-multi">Nucleic acids, one profile per fasta sequence in file</option> <option value="text">Text, single file</option> </param> <when value="amino"><!-- ffpaa --> <param name="filesin" type="data" label="Select input file(s)" format="fasta" multiple="true" /> - <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)." /> + <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)." /> </when> <when value="amino-multi"> <param name="filesin" type="data" label="Select input file(s)" format="fasta" multiple="true" /> - <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)." /> + <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)." /> </when> <when value="nucleotide"><!-- ffpry --> <param name="filesin" type="data" label="Select input file(s)" format="fasta" multiple="true" /> - <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)." /> + <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)." /> </when> <when value="nucleotide-multi"> <param name="filesin" type="data" label="Select input file(s)" format="fasta" multiple="true" /> - <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)." /> + <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)." /> </when> <when value="text"><!-- ffptxt --> @@ -200,7 +201,7 @@ <test> <param name="length" value="1"/> <param name="tree" value="0"/> - <param name="grouping" value="true"/> + <param name="groupings" value="false"/> <param name="file_type" value="nucleotide"/> <param name="filesin" value="genome1,genome2"/> <output name="info" file="test_length_1_output.tabular"/> @@ -208,11 +209,19 @@ <test> <param name="length" value="2"/> <param name="tree" value="0"/> - <param name="grouping" value="true"/> + <param name="groupings" value="false"/> <param name="file_type" value="nucleotide"/> <param name="filesin" value="genome1,genome2"/> <output name="info" file="test_length_2_output.tabular"/> </test> + <test> + <param name="length" value="2"/> + <param name="tree" value="0"/> + <param name="groupings" value="true"/> + <param name="file_type" value="nucleotide-multi"/> + <param name="filesin" value="genome1,genome2"/> + <output name="info" file="test_length_2b_output.tabular"/> + </test> </tests> <help><![CDATA[ @@ -224,7 +233,7 @@ 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. -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. +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. 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.