| Previous changeset 0:2040cda75d1f (2017-01-24) |
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Commit message:
Uploaded |
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modified:
cluster-picker.xml |
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added:
test-data/._.DS_Store test-data/dummy.fasta test-data/dummy.figTree test-data/dummy.nwk |
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| diff -r 2040cda75d1f -r 661b74ba4cc8 cluster-picker.xml --- a/cluster-picker.xml Tue Jan 24 14:09:46 2017 -0500 +++ b/cluster-picker.xml Fri Feb 03 15:26:41 2017 -0500 |
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| @@ -3,12 +3,14 @@ <requirements> <requirement type="package" version="1.2.3">cluster-picker</requirement> </requirements> -<!-- <command> <![CDATA[cluster-picker sequence_file tree_file init_threshold main_threshold dis_threshold size genetic_distance]]> </command> --> -<command> <![CDATA[cluster-picker]]> </command> +<command> <![CDATA[ln -s '$sequence_file' seq.dat && + ln -s '$tree_file' tree.dat && + cluster-picker seq.dat tree.dat $init_threshold $main_threshold $dis_threshold $size $genetic_distance + ]]> </command> <inputs> <param format="fasta" name="sequence_file" type="data" label="align" help="Please enter fasta format sequences file name to process"/> - <param format="nwk" name="tree_file" type="data" label="tree" + <param format="nhx" name="tree_file" type="data" label="tree" help="Please enter newick format tree, with branch lengths and node support"/> <param name="init_threshold" type="float" value="0.9" optional="true" help="Please enter initial support threshold for these initial subtrees" label="initial threshold"> @@ -19,13 +21,13 @@ <param name="dis_threshold" type="float" value="0.045" optional="true" help="Please enter genetic distance threshold for clusters in %" label="distance threshold"> </param> - <param name="size" type="float" value="10" optional="true" + <param name="size" type="integer" value="10" optional="true" help="To output all cluster names for clusters of size >= X enter X" label="size"> </param> <param name="genetic_distance" type="select" label="genetic distance" help="Please enter scoring type for genetic distance\n + gap = disregard sites with -, ~, or n\n abs = count absolute character differences\n - gap = disregard sites with -, ~, or n\n valid = only count differences for sites with nucleotides: a, c, t, g in both sequences\n ambiguity = disregard sites with -, ~, or n and do not count ambiguities as differences (e.g. a vs r is not a difference)"> <option value="gap">gap</option> @@ -35,20 +37,37 @@ </param> </inputs> <outputs> - <data format="figTree"/> - <data format="nhx"/> - <data format="txt"/> - <data format="fasta"/> + <data name='fig' format="figTree" from_work_dir="tree_clusterPicks.nwk.figTree"/> + <data name='tr' format="nhx" from_work_dir="tree_clusterPicks.nwk"/> + <data name='log' format="txt" from_work_dir="tree_clusterPicks_log.txt"/> + <data name='seq' format="fasta" from_work_dir="seq.dat_tree_clusterPicks.fasta"/> </outputs> <tests> - <test> - <param name="input" value="fa_gc_content_input.fa"/> - <output name="out_file1" file="fa_gc_content_output.txt"/> - </test> + <test> + <param name="sequence_file" value="dummy.fasta" /> + <param name="tree_file" value="dummy.nhx" /> + <param name="init_threshold" value="0.9" /> + <param name="main_threshold" value="0.9" /> + <param name="dis_threshold" value="0.045" /> + <param name="size" value="10" /> + <param name="genetic_distance" value="gap" /> + <param name="main_threshold" file="0.9" /> + <output name="fig" file="dummy.figTree" /> + </test> </tests> <help> Cluster identification strategies differ between studies and as a consequence cluster definitions vary. </help> +<citations> + <citation type="bibtex">@ARTICLE{cluster-picker, + author = {Ragonnet-Cronin, Manon, et al;}, + title = {Automated analysis of phylogenetic clusters}, + journal = {BMC bioinformatics}, + year = {2013}, + volume = {14.1}, + pages = {317}} + </citation> +</citations> </tool> |
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| diff -r 2040cda75d1f -r 661b74ba4cc8 test-data/._.DS_Store |
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| Binary file test-data/._.DS_Store has changed |
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| diff -r 2040cda75d1f -r 661b74ba4cc8 test-data/dummy.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dummy.fasta Fri Feb 03 15:26:41 2017 -0500 |
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| @@ -0,0 +1,8 @@ +-e >seq1 +ATTA +>seq2 +ATTA +>seq3 +ATTA +>seq4 +ATTA |
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| diff -r 2040cda75d1f -r 661b74ba4cc8 test-data/dummy.figTree --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dummy.figTree Fri Feb 03 15:26:41 2017 -0500 |
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| @@ -0,0 +1,1 @@ +#NEXUS begin taxa; dimensions ntax=4; taxlabels seq1 seq2 seq3 seq4 ; end; begin trees; tree tree_1 = [&R] (((seq1:0.001,seq2:0.002)[&support=0.0]:0.001,seq3:0.005)[&support=0.0]:0.004,seq4:0.003)[&support=0.0]:0.001; end; begin figtree; set appearance.backgroundColorAttribute="User Selection"; set appearance.backgroundColour=#-1; set appearance.branchColorAttribute="User Selection"; set appearance.branchLineWidth=1.0; set appearance.foregroundColour=#-16777216; set appearance.selectionColour=#-2144520576; set branchLabels.colorAttribute="User Selection"; set branchLabels.displayAttribute="Branch times"; set branchLabels.fontName="sansserif"; set branchLabels.fontSize=8; set branchLabels.fontStyle=0; set branchLabels.isShown=false; set branchLabels.significantDigits=4; set layout.expansion=0; set layout.layoutType="RECTILINEAR"; set layout.zoom=0; set nodeBars.barWidth=4.0; set nodeLabels.colorAttribute="User Selection"; set nodeLabels.displayAttribute="support"; set nodeLabels.fontName="Arial"; set nodeLabels.fontSize=10; set nodeLabels.fontStyle=0; set nodeLabels.isShown=true; set nodeLabels.significantDigits=3; set polarLayout.alignTipLabels=false; set polarLayout.angularRange=0; set polarLayout.rootAngle=0; set polarLayout.rootLength=100; set polarLayout.showRoot=true; set radialLayout.spread=0.0; set rectilinearLayout.alignTipLabels=false; set rectilinearLayout.curvature=0; set rectilinearLayout.rootLength=100; set scale.offsetAge=0.0; set scale.rootAge=1.0; set scale.scaleFactor=1.0; set scale.scaleRoot=false; set scaleAxis.automaticScale=true; set scaleAxis.fontSize=8.0; set scaleAxis.isShown=false; set scaleAxis.lineWidth=1.0; set scaleAxis.majorTicks=1.0; set scaleAxis.origin=0.0; set scaleAxis.reverseAxis=false; set scaleAxis.showGrid=true; set scaleAxis.significantDigits=4; set scaleBar.automaticScale=true; set scaleBar.fontSize=10.0; set scaleBar.isShown=true; set scaleBar.lineWidth=1.0; set scaleBar.scaleRange=0.0; set scaleBar.significantDigits=4; set tipLabels.colorAttribute="User Selection"; set tipLabels.displayAttribute="Names"; set tipLabels.fontName="Arial"; set tipLabels.fontSize=10; set tipLabels.fontStyle=0; set tipLabels.isShown=true; set tipLabels.significantDigits=4; set trees.order=true; set trees.orderType="increasing"; set trees.rooting=false; set trees.rootingType="User Selection"; set trees.transform=false; set trees.transformType="cladogram"; end; \ No newline at end of file |
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| diff -r 2040cda75d1f -r 661b74ba4cc8 test-data/dummy.nwk --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dummy.nwk Fri Feb 03 15:26:41 2017 -0500 |
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| @@ -0,0 +1,1 @@ +(((seq1:0.001,seq2:0.002):0.001,seq3:0.005):0.004,seq4:0.003):0.001; |