| Previous changeset 14:778f03497adb (2012-02-24) |
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Commit message:
Uploaded |
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modified:
Codonlogo.xml build_test.sh |
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added:
corebio/__init__.pyc corebio/_future/__init__.pyc corebio/_future/subprocess.pyc corebio/_version.pyc corebio/data.pyc corebio/moremath.pyc corebio/seq.pyc corebio/seq_io/__init__.pyc corebio/seq_io/_nexus/Nodes.pyc corebio/seq_io/_nexus/Trees.pyc corebio/seq_io/_nexus/__init__.pyc corebio/seq_io/array_io.pyc corebio/seq_io/clustal_io.pyc corebio/seq_io/fasta_io.pyc corebio/seq_io/genbank_io.pyc corebio/seq_io/intelligenetics_io.pyc corebio/seq_io/msf_io.pyc corebio/seq_io/nbrf_io.pyc corebio/seq_io/nexus_io.pyc corebio/seq_io/phylip_io.pyc corebio/seq_io/plain_io.pyc corebio/seq_io/stockholm_io.pyc corebio/seq_io/table_io.pyc corebio/utils/__init__.pyc corebio/utils/_which.pyc corebio/utils/deoptparse.pyc examples/Galaxy-Workflow-make6.ga weblogolib/__init__.pyc weblogolib/color.pyc weblogolib/colorscheme.pyc |
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removed:
examples/Galaxy-Workflow-Figure(1).ga |
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| diff -r 778f03497adb -r 981eb8c3a756 Codonlogo.xml --- a/Codonlogo.xml Fri Feb 24 11:37:26 2012 -0500 +++ b/Codonlogo.xml Sat Mar 31 16:07:07 2012 -0400 |
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| @@ -1,8 +1,12 @@ <tool id="codonlogo" name="Codon Logo" version="3"> <description>generator for fasta (eg Clustal alignments)</description> <command interpreter="python -W ignore::DeprecationWarning"> - codonlogo -F $outformat -s $size -f $input -o $output -t "$logoname" -m $frame -n $stacks -X $showxaxis --show-yaxis $showyaxis --errorbars $errorbars -G $strict --fineprint "$fineprint" --stack-width $stackwidth --stack-height $stackheight --box $box --resolution $resolution --scale-width $scalewidth - + codonlogo -F $outformat -s $size -f $input -o $output -m $frame -n $stacks -X $showxaxis --show-yaxis $showyaxis --errorbars $errorbars -G $strict --fineprint "$fineprint" --stack-width $stackwidth --stack-height $stackheight --box $box --resolution $resolution --scale-width $scalewidth + + #if str($logoname) != '' + -t "$logoname" + #end if + #if str($ylabel) != '' -x "$xlabel" #end if @@ -332,7 +336,7 @@ </command> <inputs> <page> - <param format="text" name="input" type="data" label="Input file.(must be an aligned fasta file of sequences the same length, recommended to use sequences aligned by codon)" /> + <param format="text" name="input" type="data" label="Input file." help="must be an aligned fasta file of sequences the same length, recommended to use sequences aligned by codon" /> <param name="logoname" label="Title for output Sequence Logo" type="text" size="50" value="" /> @@ -346,7 +350,7 @@ </param> <param name="resolution" size="5" type="integer" value="96" label="Bitmap resolution in dots per inch (DPI).For high quality printable PNG this should be set to 600" /> - <param name="frame" type="select" label="Frame to view the alignment. If reverse complement is selected then codonlogo will read from the last symbol in the sequences backwards and replace each base with it's complement." > + <param name="frame" type="select" label="Frame to view the alignment." help="If reverse complement is selected then codonlogo will read from the last symbol in the sequences backwards and replace each base with it's complement." > <option value="0" selected="True">0</option> <option value="1">+1</option> <option value="2">+2</option> @@ -409,7 +413,7 @@ <option value="Homosapiens" >Human</option> <option value="Saccharomycescerevisiae" >Yeast</option> <option value="Escherichiacoli" >E.Coli</option> - <option value="From File">from file</option> + <option value="file">from file</option> </param> <when value="auto"> @@ -419,12 +423,12 @@ <when value="none"> </when> <when value="file"> - <param format="txt" name="compfile" type="data" label="File containing the expected composition of the sequence. expected: a file with 64 codons followed by their probability. it must have 64 lines and each line must have a codon followed by a space followed by a weigt." /> + <param format="txt" name="compfile" type="data" label="File containing the expected composition of the sequence. " help="expected: a file with 64 codons followed by their probability. it must have 64 lines and each line must have a codon followed by a space followed by a weight." /> </when> </conditional> <conditional name="colours"> - <param name="colour" type="select" label="Choose colours?(it is not required to set values for all of them. Colors can be specified using CSS2 syntax. e.g. 'red', '#FF0000', etc. )"> + <param name="colour" type="select" label="Choose colours?" help="it is not required to set values for all of them. Colors can be specified using CSS2 syntax. e.g. 'red', '#FF0000', etc."> <option value="no" selected="true">Default colours</option> <option value="part">Set your own.</option> </param> |
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| diff -r 778f03497adb -r 981eb8c3a756 build_test.sh --- a/build_test.sh Fri Feb 24 11:37:26 2012 -0500 +++ b/build_test.sh Sat Mar 31 16:07:07 2012 -0400 |
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| b'@@ -1,110 +1,110 @@\n \n mkdir -p tmp\n \n-echo "# Test weblogo by building logos with many different options."\n+echo "# Test codonlogo by building logos with many different options."\n \n echo -ne \'.\'\n-./weblogo < cap.fa > tmp/logo0.eps ||exit\n+./codonlogo < cap.fa > tmp/logo0.eps ||exit\n \n echo -ne \'.\'\n-./weblogo --title "Default Logo with Title" < cap.fa > tmp/logo1.eps ||exit\n+./codonlogo --title "Default Logo with Title" < cap.fa > tmp/logo1.eps ||exit\n \n echo -ne \'.\'\n-./weblogo --debug yes --fineprint "Default Logo with this fineprint and debug on" < cap.fa > tmp/logo2.eps ||exit\n+./codonlogo --debug yes --fineprint "Default Logo with this fineprint and debug on" < cap.fa > tmp/logo2.eps ||exit\n \n echo -ne \'.\'\n-./weblogo --debug no --fineprint "--debug no" --debug no < cap.fa > tmp/logo3.eps ||exit\n+./codonlogo --debug no --fineprint "--debug no" --debug no < cap.fa > tmp/logo3.eps ||exit\n \n echo -ne \'.\'\n-./weblogo --debug yes --fineprint "" --title "No fine print" --debug yes < cap.fa > tmp/logo4.eps ||exit\n+./codonlogo --debug yes --fineprint "" --title "No fine print" --debug yes < cap.fa > tmp/logo4.eps ||exit\n \n echo -ne \'.\'\n-./weblogo --debug yes --fineprint "No title" --title "" < cap.fa > tmp/logo5.eps ||exit\n+./codonlogo --debug yes --fineprint "No title" --title "" < cap.fa > tmp/logo5.eps ||exit\n \n echo -ne \'.\'\n-./weblogo --debug yes --fineprint "--first-index -10" --first-index -10 < cap.fa > tmp/logo6.eps ||exit\n+./codonlogo --debug yes --fineprint "--first-index -10" --first-index -10 < cap.fa > tmp/logo6.eps ||exit\n \n echo -ne \'.\'\n-./weblogo --debug yes --fineprint " --first-index -10 --stacks-per-line 11 " --first-index -10 --stacks-per-line 11 < cap.fa > tmp/logo7a.eps ||exit\n+./codonlogo --debug yes --fineprint " --first-index -10 --stacks-per-line 11 " --first-index -10 --stacks-per-line 11 < cap.fa > tmp/logo7a.eps ||exit\n \n echo -ne \'.\'\n-./weblogo --debug yes --fineprint " --first-index -10 --stacks-per-line 8 " --first-index -10 --stacks-per-line 8 < cap.fa > tmp/logo7b.eps ||exit\n+./codonlogo --debug yes --fineprint " --first-index -10 --stacks-per-line 8 " --first-index -10 --stacks-per-line 8 < cap.fa > tmp/logo7b.eps ||exit\n \n echo -ne \'.\'\n-./weblogo --debug yes --fineprint " --first-index -10 --stacks-per-line 7 " --first-index -10 --stacks-per-line 7 < cap.fa > tmp/logo7c.eps ||exit\n+./codonlogo --debug yes --fineprint " --first-index -10 --stacks-per-line 7 " --first-index -10 --stacks-per-line 7 < cap.fa > tmp/logo7c.eps ||exit\n \n echo -ne \'.\'\n-./weblogo --debug yes --fineprint "Test fin and fout" --fin cap.fa --fout logo8.eps ||exit\n+./codonlogo --debug yes --fineprint "Test fin and fout" --fin cap.fa --fout logo8.eps ||exit\n \n # Test Y Axis\n \n echo -ne \'.\'\n-./weblogo --debug yes --fineprint "Custom yaxis label " --ylabel \'yaxis label\' < cap.fa > tmp/logo9a.eps ||exit\n+./codonlogo --debug yes --fineprint "Custom yaxis label " --ylabel \'yaxis label\' < cap.fa > tmp/logo9a.eps ||exit\n \n echo -ne \'.\'\n-./weblogo --debug yes --fineprint "Custom units" --units \'nats\' < cap.fa > tmp/logo9b.eps ||exit\n+./codonlogo --debug yes --fineprint "Custom units" --units \'nats\' < cap.fa > tmp/logo9b.eps ||exit\n \n echo -ne \'.\'\n-./weblogo --debug yes --fineprint "Override custom units with custom yaxis label." --ylabel \'yaxis label\' --units nats < cap.fa > tmp/logo9c.eps ||exit\n+./codonlogo --debug yes --fineprint "Override custom units with custom yaxis label." --ylabel \'yaxis label\' --units nats < cap.fa > tmp/logo9c.eps ||exit\n \n echo -ne \'.\'\n-./weblogo --debug yes --fineprint "Empty ylabel" --ylabel \'\' < cap.fa > tmp/logo9d.eps\n+./codonlogo --debug yes --fineprint "Empty ylabel" --ylabel \'\' < cap.fa > tmp/logo9d.eps\n \n echo -ne \'.\'\n-./weblogo --debug yes --fineprint "No Yaxis" --show-yaxis no < cap.fa > tmp/logo9e.eps ||exit\n+./codonlogo --debug yes --fineprint "No Yaxis" --show-yaxis no < cap.fa > tmp/logo9e.eps ||exit\n \n # Test X Axis\n \n echo -ne \'.\'\n-./weblogo --debug yes --format pdf --finep'..b'\'.\'\n-./weblogo --debug yes --format pdf --fineprint "No Xaxis" --show-xaxis no < cap.fa > tmp/logo10c.pdf ||exit\n+./codonlogo --debug yes --format pdf --fineprint "No Xaxis" --show-xaxis no < cap.fa > tmp/logo10c.pdf ||exit\n \n echo -ne \'.\'\n-./weblogo --debug yes --format pdf --fineprint "No Xaxis, custom label" --xlabel "Custom xlabel" --show-xaxis no < cap.fa > tmp/logo10d.pdf ||exit\n+./codonlogo --debug yes --format pdf --fineprint "No Xaxis, custom label" --xlabel "Custom xlabel" --show-xaxis no < cap.fa > tmp/logo10d.pdf ||exit\n \n # Test Formats\n \n echo -ne \'.\'\n-./weblogo --debug no --fineprint "Format: eps" --format eps < cap.fa > tmp/logo11a.eps ||exit\n+./codonlogo --debug no --fineprint "Format: eps" --format eps < cap.fa > tmp/logo11a.eps ||exit\n \n echo -ne \'.\'\n-./weblogo --debug no --fineprint "Format: png" --size large --format png < cap.fa > tmp/logo11b.png ||exit\n+./codonlogo --debug no --fineprint "Format: png" --size large --format png < cap.fa > tmp/logo11b.png ||exit\n \n echo -ne \'.\'\n-./weblogo --debug no --fineprint "Format: png high res" --format png_print < cap.fa > tmp/logo11c.png ||exit\n+./codonlogo --debug no --fineprint "Format: png high res" --format png_print < cap.fa > tmp/logo11c.png ||exit\n \n echo -ne \'.\'\n-./weblogo --debug no --fineprint "Format: pdf" --format pdf < cap.fa > tmp/logo11d.pdf ||exit\n+./codonlogo --debug no --fineprint "Format: pdf" --format pdf < cap.fa > tmp/logo11d.pdf ||exit\n \n echo -ne \'.\'\n-./weblogo --debug no --fineprint "Format: jpeg" --size large --format jpeg < cap.fa > tmp/logo11e.jpeg ||exit\n+./codonlogo --debug no --fineprint "Format: jpeg" --size large --format jpeg < cap.fa > tmp/logo11e.jpeg ||exit\n \n echo -ne \'.\'\n-./weblogo --debug no --fineprint "Format: EPS" --format EPS < cap.fa > tmp/logo11f.eps ||exit\n+./codonlogo --debug no --fineprint "Format: EPS" --format EPS < cap.fa > tmp/logo11f.eps ||exit\n \n # Test Sizes\n \n echo -ne \'.\'\n-./weblogo --debug no --format png_print --fineprint "default size" < cap.fa > tmp/logo12_default.png ||exit\n+./codonlogo --debug no --format png_print --fineprint "default size" < cap.fa > tmp/logo12_default.png ||exit\n \n echo -ne \'.\'\n-./weblogo --debug no --format png_print --fineprint "--size large" --size large < cap.fa > tmp/logo12_large.png ||exit\n+./codonlogo --debug no --format png_print --fineprint "--size large" --size large < cap.fa > tmp/logo12_large.png ||exit\n \n echo -ne \'.\'\n-./weblogo --debug no --format png_print --fineprint "--size medium" --size medium < cap.fa > tmp/logo12_medium.png ||exit\n+./codonlogo --debug no --format png_print --fineprint "--size medium" --size medium < cap.fa > tmp/logo12_medium.png ||exit\n \n echo -ne \'.\'\n-./weblogo --debug no --format png_print --fineprint "--size small" --size small < cap.fa > tmp/logo12_small.png ||exit\n+./codonlogo --debug no --format png_print --fineprint "--size small" --size small < cap.fa > tmp/logo12_small.png ||exit\n \n \n \n echo -ne \'.\'\n-./weblogo --format pdf --fineprint "" > tmp/logo13.pdf << LimitString\n+./codonlogo --format pdf --fineprint "" > tmp/logo13.pdf << LimitString\n >\n GTTGTTGTTGTT\n >\n@@ -120,25 +120,7 @@\n \n # Test unit options\n echo -ne \'.\'\n-./weblogo --format pdf --fineprint "probability" --unit probability > tmp/logo14a.pdf < cap.fa ||exit\n-\n-echo -ne \'.\'\n-./weblogo --format pdf --fineprint "bits" --unit bits > tmp/logo14b.pdf < cap.fa ||exit\n-\n-echo -ne \'.\'\n-./weblogo --format pdf --fineprint "nats" --unit nats > tmp/logo14c.pdf < cap.fa ||exit\n-\n-echo -ne \'.\'\n-./weblogo --format pdf --fineprint "kJ/mol" --unit kJ/mol \\\n- > tmp/logo14d.pdf < cap.fa ||exit\n-\n-echo -ne \'.\'\n-./weblogo --format pdf --fineprint "kT" --unit kT \\\n- > tmp/logo14e.pdf < cap.fa ||exit\n-\n-echo -ne \'.\'\n-./weblogo --format pdf --fineprint "kcal/mol" --unit kcal/mol \\\n- > tmp/logo14f.pdf < cap.fa || exit\n+./codonlogo --format pdf --fineprint "probability" --unit probability > tmp/logo14a.pdf < cap.fa ||exit\n \n \n \n@@ -146,3 +128,4 @@\n \n \n \n+\n' |
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| diff -r 778f03497adb -r 981eb8c3a756 examples/Galaxy-Workflow-Figure(1).ga --- a/examples/Galaxy-Workflow-Figure(1).ga Fri Feb 24 11:37:26 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,118 +0,0 @@ -{ - "a_galaxy_workflow": "true", - "annotation": "Generates part B", - "format-version": "0.1", - "name": "Figure", - "steps": { - "0": { - "annotation": "", - "id": 0, - "input_connections": {}, - "inputs": [ - { - "description": "", - "name": "Input Dataset" - } - ], - "name": "Input dataset", - "outputs": [], - "position": { - "left": 197, - "top": 384 - }, - "tool_errors": null, - "tool_id": null, - "tool_state": "{\"name\": \"Input Dataset\"}", - "tool_version": null, - "type": "data_input", - "user_outputs": [] - }, - "1": { - "annotation": "", - "id": 1, - "input_connections": { - "input": { - "id": 0, - "output_name": "output" - } - }, - "inputs": [], - "name": "Codon Logo", - "outputs": [ - { - "name": "output", - "type": "pdf" - } - ], - "position": { - "left": 580, - "top": 228 - }, - "post_job_actions": {}, - "tool_errors": null, - "tool_id": "codonlogo", - "tool_state": "{\"outformat\": \"\\\"pdf\\\"\", \"frame\": \"\\\"0\\\"\", \"size\": \"\\\"large\\\"\", \"__page__\": 0, \"colours\": \"{\\\"colour\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"strict\": \"\\\"False\\\"\", \"logoname\": \"\\\"0 Frame\\\"\", \"ylabel\": \"\\\"\\\"\", \"input\": \"null\", \"stackheight\": \"\\\"100\\\"\", \"scalewidth\": \"\\\"True\\\"\", \"showyaxis\": \"\\\"True\\\"\", \"comp\": \"{\\\"mode\\\": \\\"equiprobable\\\", \\\"__current_case__\\\": 1}\", \"showxaxis\": \"\\\"True\\\"\", \"stackwidth\": \"\\\"40.0\\\"\", \"box\": \"\\\"False\\\"\", \"fineprint\": \"\\\"\\\"\", \"range\": \"{\\\"seqend\\\": \\\"16\\\", \\\"mode\\\": \\\"part\\\", \\\"__current_case__\\\": 1, \\\"seqstart\\\": \\\"6\\\"}\", \"xlabel\": \"\\\"\\\"\", \"errorbars\": \"\\\"True\\\"\", \"resolution\": \"\\\"96\\\"\", \"stacks\": \"\\\"20\\\"\"}", - "tool_version": "3", - "type": "tool", - "user_outputs": [] - }, - "2": { - "annotation": "", - "id": 2, - "input_connections": { - "input": { - "id": 0, - "output_name": "output" - } - }, - "inputs": [], - "name": "Codon Logo", - "outputs": [ - { - "name": "output", - "type": "pdf" - } - ], - "position": { - "left": 580, - "top": 360 - }, - "post_job_actions": {}, - "tool_errors": null, - "tool_id": "codonlogo", - "tool_state": "{\"outformat\": \"\\\"pdf\\\"\", \"frame\": \"\\\"1\\\"\", \"size\": \"\\\"large\\\"\", \"__page__\": 0, \"colours\": \"{\\\"colour\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"strict\": \"\\\"False\\\"\", \"logoname\": \"\\\"+1 Frame\\\"\", \"ylabel\": \"\\\"\\\"\", \"input\": \"null\", \"stackheight\": \"\\\"100\\\"\", \"scalewidth\": \"\\\"True\\\"\", \"showyaxis\": \"\\\"True\\\"\", \"comp\": \"{\\\"mode\\\": \\\"equiprobable\\\", \\\"__current_case__\\\": 1}\", \"showxaxis\": \"\\\"True\\\"\", \"stackwidth\": \"\\\"40.0\\\"\", \"box\": \"\\\"False\\\"\", \"fineprint\": \"\\\"\\\"\", \"range\": \"{\\\"seqend\\\": \\\"16\\\", \\\"mode\\\": \\\"part\\\", \\\"__current_case__\\\": 1, \\\"seqstart\\\": \\\"6\\\"}\", \"xlabel\": \"\\\"\\\"\", \"errorbars\": \"\\\"True\\\"\", \"resolution\": \"\\\"96\\\"\", \"stacks\": \"\\\"20\\\"\"}", - "tool_version": "3", - "type": "tool", - "user_outputs": [] - }, - "3": { - "annotation": "", - "id": 3, - "input_connections": { - "input": { - "id": 0, - "output_name": "output" - } - }, - "inputs": [], - "name": "Codon Logo", - "outputs": [ - { - "name": "output", - "type": "pdf" - } - ], - "position": { - "left": 580, - "top": 493 - }, - "post_job_actions": {}, - "tool_errors": null, - "tool_id": "codonlogo", - "tool_state": "{\"outformat\": \"\\\"pdf\\\"\", \"frame\": \"\\\"2\\\"\", \"size\": \"\\\"large\\\"\", \"__page__\": 0, \"colours\": \"{\\\"colour\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"strict\": \"\\\"False\\\"\", \"logoname\": \"\\\"+2 Frame\\\"\", \"ylabel\": \"\\\"\\\"\", \"input\": \"null\", \"stackheight\": \"\\\"100\\\"\", \"scalewidth\": \"\\\"True\\\"\", \"showyaxis\": \"\\\"True\\\"\", \"comp\": \"{\\\"mode\\\": \\\"equiprobable\\\", \\\"__current_case__\\\": 1}\", \"showxaxis\": \"\\\"True\\\"\", \"stackwidth\": \"\\\"40.0\\\"\", \"box\": \"\\\"False\\\"\", \"fineprint\": \"\\\"\\\"\", \"range\": \"{\\\"seqend\\\": \\\"16\\\", \\\"mode\\\": \\\"part\\\", \\\"__current_case__\\\": 1, \\\"seqstart\\\": \\\"6\\\"}\", \"xlabel\": \"\\\"\\\"\", \"errorbars\": \"\\\"True\\\"\", \"resolution\": \"\\\"96\\\"\", \"stacks\": \"\\\"20\\\"\"}", - "tool_version": "3", - "type": "tool", - "user_outputs": [] - } - } -} \ No newline at end of file |
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| diff -r 778f03497adb -r 981eb8c3a756 examples/Galaxy-Workflow-make6.ga --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/examples/Galaxy-Workflow-make6.ga Sat Mar 31 16:07:07 2012 -0400 |
| [ |
| b'@@ -0,0 +1,205 @@\n+{\n+ "a_galaxy_workflow": "true", \n+ "annotation": "Creates 6 codon logos, one for each frame and one for each frame of the reverse complement.", \n+ "format-version": "0.1", \n+ "name": "make6", \n+ "steps": {\n+ "0": {\n+ "annotation": "", \n+ "id": 0, \n+ "input_connections": {}, \n+ "inputs": [\n+ {\n+ "description": "", \n+ "name": "Input Dataset"\n+ }\n+ ], \n+ "name": "Input dataset", \n+ "outputs": [], \n+ "position": {\n+ "left": 148, \n+ "top": 194.5\n+ }, \n+ "tool_errors": null, \n+ "tool_id": null, \n+ "tool_state": "{\\"name\\": \\"Input Dataset\\"}", \n+ "tool_version": null, \n+ "type": "data_input", \n+ "user_outputs": []\n+ }, \n+ "1": {\n+ "annotation": "", \n+ "id": 1, \n+ "input_connections": {\n+ "input": {\n+ "id": 0, \n+ "output_name": "output"\n+ }\n+ }, \n+ "inputs": [], \n+ "name": "Codon Logo", \n+ "outputs": [\n+ {\n+ "name": "output", \n+ "type": "pdf"\n+ }\n+ ], \n+ "position": {\n+ "left": 555.5, \n+ "top": 200\n+ }, \n+ "post_job_actions": {}, \n+ "tool_errors": null, \n+ "tool_id": "codonlogo", \n+ "tool_state": "{\\"outformat\\": \\"\\\\\\"png\\\\\\"\\", \\"frame\\": \\"\\\\\\"0\\\\\\"\\", \\"size\\": \\"\\\\\\"large\\\\\\"\\", \\"__page__\\": 0, \\"colours\\": \\"{\\\\\\"colour\\\\\\": \\\\\\"no\\\\\\", \\\\\\"__current_case__\\\\\\": 0}\\", \\"strict\\": \\"\\\\\\"False\\\\\\"\\", \\"logoname\\": \\"\\\\\\"0 Frame\\\\\\"\\", \\"ylabel\\": \\"\\\\\\"\\\\\\"\\", \\"input\\": \\"null\\", \\"stackheight\\": \\"\\\\\\"100\\\\\\"\\", \\"scalewidth\\": \\"\\\\\\"True\\\\\\"\\", \\"showyaxis\\": \\"\\\\\\"True\\\\\\"\\", \\"comp\\": \\"{\\\\\\"mode\\\\\\": \\\\\\"none\\\\\\", \\\\\\"__current_case__\\\\\\": 2}\\", \\"showxaxis\\": \\"\\\\\\"True\\\\\\"\\", \\"stackwidth\\": \\"\\\\\\"40.0\\\\\\"\\", \\"box\\": \\"\\\\\\"False\\\\\\"\\", \\"fineprint\\": \\"\\\\\\"CodonLogo 1.1\\\\\\"\\", \\"range\\": \\"{\\\\\\"mode\\\\\\": \\\\\\"complete\\\\\\", \\\\\\"__current_case__\\\\\\": 0}\\", \\"xlabel\\": \\"\\\\\\"\\\\\\"\\", \\"errorbars\\": \\"\\\\\\"True\\\\\\"\\", \\"resolution\\": \\"\\\\\\"96\\\\\\"\\", \\"stacks\\": \\"\\\\\\"20\\\\\\"\\"}", \n+ "tool_version": "3", \n+ "type": "tool", \n+ "user_outputs": []\n+ }, \n+ "2": {\n+ "annotation": "", \n+ "id": 2, \n+ "input_connections": {\n+ "input": {\n+ "id": 0, \n+ "output_name": "output"\n+ }\n+ }, \n+ "inputs": [], \n+ "name": "Codon Logo", \n+ "outputs": [\n+ {\n+ "name": "output", \n+ "type": "pdf"\n+ }\n+ ], \n+ "position": {\n+ "left": 555.5, \n+ "top": 281\n+ }, \n+ "post_job_actions": {}, \n+ "tool_errors": null, \n+ "tool_id": "codonlogo", \n+ "tool_state": "{\\"outformat\\": \\"\\\\\\"png\\\\\\"\\", \\"frame\\": \\"\\\\\\"1\\\\\\"\\", \\"size\\": \\"\\\\\\"large\\\\\\"\\", \\"__page__\\": 0, \\"colours\\": \\"{\\\\\\"colour\\\\\\": \\\\\\"no\\\\\\", \\\\\\"__current_case__\\\\\\": 0}\\", \\"strict\\": \\"\\\\\\"False\\\\\\"\\", \\"logoname\\": \\"\\\\\\"+1 Frame\\\\\\"\\", \\"ylabel\\": \\"\\\\\\"\\\\\\"\\", \\"input\\": \\"null\\", \\"stackheight\\": \\"\\\\\\"100\\\\\\"\\", \\"scalewidth\\": \\"\\\\\\"True\\\\\\"\\", \\"showyaxis\\": \\"\\\\\\"True\\\\\\"\\", \\"comp\\": \\"{\\\\\\"mode\\\\\\": \\\\\\"none\\\\\\", \\\\\\"__current_case__\\\\\\": 2}\\", \\"showxaxis\\": \\"\\\\\\"True\\\\\\"\\", \\"stackwidth\\": \\"\\\\\\"40.0\\\\\\"\\", \\"box\\": \\"\\\\\\"False\\\\\\"\\", \\"fineprint\\": \\"\\\\\\"CodonLogo 1.1\\\\\\"\\", \\"range\\": \\"{\\\\\\"mode\\\\\\": \\\\\\"complete\\\\\\", \\\\\\"__current_case__\\\\\\": 0}\\", \\"xlabel\\": \\"\\\\\\"\\\\\\"\\", \\"errorbars\\": \\"\\'..b'", \\"ylabel\\": \\"\\\\\\"\\\\\\"\\", \\"input\\": \\"null\\", \\"stackheight\\": \\"\\\\\\"100\\\\\\"\\", \\"scalewidth\\": \\"\\\\\\"True\\\\\\"\\", \\"showyaxis\\": \\"\\\\\\"True\\\\\\"\\", \\"comp\\": \\"{\\\\\\"mode\\\\\\": \\\\\\"none\\\\\\", \\\\\\"__current_case__\\\\\\": 2}\\", \\"showxaxis\\": \\"\\\\\\"True\\\\\\"\\", \\"stackwidth\\": \\"\\\\\\"40.0\\\\\\"\\", \\"box\\": \\"\\\\\\"False\\\\\\"\\", \\"fineprint\\": \\"\\\\\\"CodonLogo 1.1\\\\\\"\\", \\"range\\": \\"{\\\\\\"mode\\\\\\": \\\\\\"complete\\\\\\", \\\\\\"__current_case__\\\\\\": 0}\\", \\"xlabel\\": \\"\\\\\\"\\\\\\"\\", \\"errorbars\\": \\"\\\\\\"True\\\\\\"\\", \\"resolution\\": \\"\\\\\\"96\\\\\\"\\", \\"stacks\\": \\"\\\\\\"20\\\\\\"\\"}", \n+ "tool_version": "3", \n+ "type": "tool", \n+ "user_outputs": []\n+ }, \n+ "5": {\n+ "annotation": "", \n+ "id": 5, \n+ "input_connections": {\n+ "input": {\n+ "id": 0, \n+ "output_name": "output"\n+ }\n+ }, \n+ "inputs": [], \n+ "name": "Codon Logo", \n+ "outputs": [\n+ {\n+ "name": "output", \n+ "type": "pdf"\n+ }\n+ ], \n+ "position": {\n+ "left": 550.5, \n+ "top": 549\n+ }, \n+ "post_job_actions": {}, \n+ "tool_errors": null, \n+ "tool_id": "codonlogo", \n+ "tool_state": "{\\"outformat\\": \\"\\\\\\"png\\\\\\"\\", \\"frame\\": \\"\\\\\\"4\\\\\\"\\", \\"size\\": \\"\\\\\\"large\\\\\\"\\", \\"__page__\\": 0, \\"colours\\": \\"{\\\\\\"colour\\\\\\": \\\\\\"no\\\\\\", \\\\\\"__current_case__\\\\\\": 0}\\", \\"strict\\": \\"\\\\\\"False\\\\\\"\\", \\"logoname\\": \\"\\\\\\"+1 Frame Reverse Complement\\\\\\"\\", \\"ylabel\\": \\"\\\\\\"\\\\\\"\\", \\"input\\": \\"null\\", \\"stackheight\\": \\"\\\\\\"100\\\\\\"\\", \\"scalewidth\\": \\"\\\\\\"True\\\\\\"\\", \\"showyaxis\\": \\"\\\\\\"True\\\\\\"\\", \\"comp\\": \\"{\\\\\\"mode\\\\\\": \\\\\\"none\\\\\\", \\\\\\"__current_case__\\\\\\": 2}\\", \\"showxaxis\\": \\"\\\\\\"True\\\\\\"\\", \\"stackwidth\\": \\"\\\\\\"40.0\\\\\\"\\", \\"box\\": \\"\\\\\\"False\\\\\\"\\", \\"fineprint\\": \\"\\\\\\"CodonLogo 1.1\\\\\\"\\", \\"range\\": \\"{\\\\\\"mode\\\\\\": \\\\\\"complete\\\\\\", \\\\\\"__current_case__\\\\\\": 0}\\", \\"xlabel\\": \\"\\\\\\"\\\\\\"\\", \\"errorbars\\": \\"\\\\\\"True\\\\\\"\\", \\"resolution\\": \\"\\\\\\"96\\\\\\"\\", \\"stacks\\": \\"\\\\\\"20\\\\\\"\\"}", \n+ "tool_version": "3", \n+ "type": "tool", \n+ "user_outputs": []\n+ }, \n+ "6": {\n+ "annotation": "", \n+ "id": 6, \n+ "input_connections": {\n+ "input": {\n+ "id": 0, \n+ "output_name": "output"\n+ }\n+ }, \n+ "inputs": [], \n+ "name": "Codon Logo", \n+ "outputs": [\n+ {\n+ "name": "output", \n+ "type": "pdf"\n+ }\n+ ], \n+ "position": {\n+ "left": 548.5, \n+ "top": 644\n+ }, \n+ "post_job_actions": {}, \n+ "tool_errors": null, \n+ "tool_id": "codonlogo", \n+ "tool_state": "{\\"outformat\\": \\"\\\\\\"png\\\\\\"\\", \\"frame\\": \\"\\\\\\"5\\\\\\"\\", \\"size\\": \\"\\\\\\"large\\\\\\"\\", \\"__page__\\": 0, \\"colours\\": \\"{\\\\\\"colour\\\\\\": \\\\\\"no\\\\\\", \\\\\\"__current_case__\\\\\\": 0}\\", \\"strict\\": \\"\\\\\\"False\\\\\\"\\", \\"logoname\\": \\"\\\\\\"-1 Frame Reverse Complement\\\\\\"\\", \\"ylabel\\": \\"\\\\\\"\\\\\\"\\", \\"input\\": \\"null\\", \\"stackheight\\": \\"\\\\\\"100\\\\\\"\\", \\"scalewidth\\": \\"\\\\\\"True\\\\\\"\\", \\"showyaxis\\": \\"\\\\\\"True\\\\\\"\\", \\"comp\\": \\"{\\\\\\"mode\\\\\\": \\\\\\"none\\\\\\", \\\\\\"__current_case__\\\\\\": 2}\\", \\"showxaxis\\": \\"\\\\\\"True\\\\\\"\\", \\"stackwidth\\": \\"\\\\\\"40.0\\\\\\"\\", \\"box\\": \\"\\\\\\"False\\\\\\"\\", \\"fineprint\\": \\"\\\\\\"CodonLogo 1.1\\\\\\"\\", \\"range\\": \\"{\\\\\\"mode\\\\\\": \\\\\\"complete\\\\\\", \\\\\\"__current_case__\\\\\\": 0}\\", \\"xlabel\\": \\"\\\\\\"\\\\\\"\\", \\"errorbars\\": \\"\\\\\\"True\\\\\\"\\", \\"resolution\\": \\"\\\\\\"96\\\\\\"\\", \\"stacks\\": \\"\\\\\\"20\\\\\\"\\"}", \n+ "tool_version": "3", \n+ "type": "tool", \n+ "user_outputs": []\n+ }\n+ }\n+}\n\\ No newline at end of file\n' |
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