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Commit message:
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab" |
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added:
macros.xml replace.xml test-data/Animals_More.csv test-data/XY_converted.csv test-data/XY_converted.tsv test-data/XY_with_break.csv test-data/XY_with_break.tabular test-data/another.csv test-data/awk_mutate_input.csv test-data/awk_mutate_output.csv test-data/blood_type.tsv test-data/collapsed.tsv test-data/concat_1.csv test-data/concat_2.csv test-data/corr_1.csv test-data/corr_2.tsv test-data/csv-bob.csv test-data/csv-darian.csv test-data/csv-jack.csv test-data/csv.csv test-data/cut_1.csv test-data/cut_2.csv test-data/data.csv test-data/filtered.tsv test-data/frequency.tsv test-data/gathered.csv test-data/illegal.csv test-data/illegal_collapse.csv test-data/joined.csv test-data/joined_filled.csv test-data/kv.txt test-data/line_all_param.png test-data/mutate_removed.tsv test-data/mutated.tsv test-data/other.csv test-data/plot.csv test-data/plot.png test-data/plot_box.png test-data/plot_scatter.png test-data/replace_1.csv test-data/replace_2.csv test-data/replace_input.csv test-data/sampled_1.csv test-data/sampled_2.csv test-data/separated_1.tsv test-data/separated_2.tsv test-data/sort_order.txt test-data/sorted_1.csv test-data/test.csv test-data/uniq.tsv |
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| diff -r 000000000000 -r 1d4ee4308d99 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue May 19 17:16:05 2020 -0400 |
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| b'@@ -0,0 +1,337 @@\n+<macros>\n+ <token name="@VERSION@">0.20.0</token>\n+ <token name="@GALAXY_VERSION@">galaxy0</token>\n+ <xml name="requirements">\n+ <requirements>\n+ <requirement type="package" version="@VERSION@">csvtk</requirement>\n+ </requirements>\n+ </xml>\n+ <xml name="version_cmd">\n+ <version_command>csvtk version</version_command>\n+ </xml>\n+ <xml name="text_sanitizer">\n+ <sanitizer>\n+ <valid initial="string.printable">\n+ <remove value="'"/>\n+ </valid>\n+ </sanitizer>\n+ </xml>\n+ <xml name="multi_input">\n+ <param type="data" name="in_1" format="csv,tabular"\n+ multiple="true" optional="false"\n+ label="Specify TSV or CSV file inputs"\n+ help="Input tsv or csv files to analyze. HOWEVER, they must all be the **same file type** or the tool will fail/not give correct results!"\n+ />\n+ </xml>\n+ <xml name="singular_input">\n+ <param type="data" name="in_1" format="csv,tabular"\n+ multiple="false" optional="false"\n+ label="Specify an input TSV or CSV file"\n+ help="Input a TSV or CSV file to work on"\n+ />\n+ </xml>\n+ <xml name="ignore_case">\n+ <param type="boolean" name="ignore_case"\n+ falsevalue="" truevalue="-i"\n+ checked="false"\n+ argument="-i"\n+ label="Ignore cell case?"\n+ help="ABC == abc"\n+ />\n+ </xml>\n+ <xml name="global_parameters">\n+ <section name="global_param" title="csvtk Global Parameters" expanded="false">\n+ <param type="boolean" name="header"\n+ falsevalue="-H" truevalue=""\n+ checked="true"\n+ argument="-H"\n+ label="Input file has a header line"\n+ />\n+ <param type="boolean" name="illegal_rows"\n+ falsevalue="" truevalue="-I"\n+ checked="false"\n+ argument="-I"\n+ label="Ignore illegal rows"\n+ help="Use if file has illegal rows as defined in the help section"\n+ />\n+ <param type="boolean" name="empty_rows"\n+ falsevalue="" truevalue="-E"\n+ checked="false"\n+ argument="-E"\n+ label="Ignore empty rows"\n+ help="Ignore rows with no data (only needed if input has empty rows)"\n+ />\n+ <param type="boolean" name="lazy_quotes"\n+ falsevalue="" truevalue="-l"\n+ checked="false"\n+ argument="-l"\n+ label="File has Lazy quotes"\n+ help="(TSV files only) If Yes, a quote may appear in an unquoted field and a non-doubled quote may appear in a quoted field"\n+ />\n+ </section>\n+ </xml>\n+ <xml name="fields_input">\n+ <conditional name="column_text" >\n+ <param type="select" name="select" label="Select input column(s) based on" argument="-F -f">\n+ <option value="string">Column Name(s)</option>\n+ <option value="column">Column Number(s)</option>\n+ </param>\n+ <when value="column">\n+ <param type="data_column" name="in_text"\n+ data_ref="in_1"\n+ multiple="true"\n+ label="Input column number(s)"\n+ help="Select column(s) to use for analysis"\n+ />\n+ </when>\n+ <when value="string">\n+ <param type="text" name="in_text"\n+ optional="false"\n+ label="Input column name(s)"\n+ help="Multiple columns can be given if separated by a \' , \'. \n+ Column numbers can be given too - ex. \'1,2\' will target columns 1 and 2. \n+ Please see the help section below for more detailed info">\n+ <sanit'..b' <sanitizer>\n+ <valid initial="string.printable">\n+ <remove value="'"/>\n+ </valid>\n+ </sanitizer>\n+ </param>\n+ <param type="float" name="min_x"\n+ argument="--x-min"\n+ optional="true"\n+ label="Minimum value of X-axis (float)"\n+ />\n+ <param type="float" name="max_x"\n+ argument="--x-max"\n+ optional="true"\n+ label="Maximum value of X-axis (float)"\n+ />\n+ <param type="text" name="y_label"\n+ argument="--ylab"\n+ optional="true"\n+ label="Specify Y-axis label">\n+ <sanitizer>\n+ <valid initial="string.printable">\n+ <remove value="'"/>\n+ </valid>\n+ </sanitizer>\n+ </param>\n+ <param type="float" name="min_y"\n+ argument="--y-min"\n+ optional="true"\n+ label="Minimum value of Y-axis (float)"\n+ />\n+ <param type="float" name="max_y"\n+ argument="--y-max"\n+ optional="true"\n+ label="Maximum value of Y-axis (float)"\n+ />\n+ </section>\n+ </xml>\n+ <token name="@HELP_COLUMNS@">\n+Column Name Input Help\n+######################\n+\n+- Multiple names can be given if separated by a \' , \'.\n+\n+ - ex. \'ID,Organism\' would target the columns named ID and Organism for the function \n+\n+- Column names are case SeNsitive\n+\n+- Column numbers can also be given:\n+\n+ -ex. \'1,2,3\' or \'1-3\' for inputting columns 1-3.\n+\n+- You can also specify all but unwanted column(s) with a \' - \'.\n+\n+ - ex. \'-ID\' would target all columns but the ID column\n+\n+----\n+ </token>\n+ <token name="@HELP_INPUT_DATA@">\n+Input Data\n+##########\n+\n+::\n+\n+ **Limitations of Input Data**\n+\n+ 1. The CSV parser requires all the lines have same number of fields/columns.\n+ If your file has illegal rows, set the "Illegal Rows" parameter to "Yes" to pass your data through\n+ Even lines with spaces will cause error.\n+ Example bad table below.\n+\n+ 2. By default, csvtk thinks files have header rows. If your file does not, set global parameter\n+ "Has Header Row" to "No"\n+\n+ 3. Column names should be unique and are case sensitive!\n+\n+ 4. Lines starting with "#" or "$" will be ignored, if in the header row\n+\n+ 5. If " exists in tab-delimited files, set Lazy quotes global parameter to "Yes"\n+\n+Example bad table:\n+\n++--------+--------+--------+--------+\n+| Head 1 | Head 2 | Head 3 | Head 3 |\n++========+========+========+========+\n+| 1 | 2 | 3 | |\n++--------+--------+--------+--------+\n+| this | will | | break |\n++--------+--------+--------+--------+\n+\n+Bad tables may work if both the "Ignore Illegal Rows" and "Ignore Empty Rows" global parameters are set to "Yes",\n+But there is no guarentee of that!\n+\n+----\n+ </token>\n+ <token name="@HELP_END_STATEMENT@">\n+More Information\n+################\n+For information from the creators of csvtk, please visit their site at: https://bioinf.shenwei.me/csvtk/\n+\n+Although be aware that some features may not be available and some small changes were made to work with Galaxy.\n+\n+**Notable changes from their documentation:**\n+\n+- Cannot specify multiple file header names (IE cannot use "name;username" as a valid column match)\n+\n+- No single quotes / apostrophes allowed in text inputs\n+ </token>\n+ <xml name="citations">\n+ <citations>\n+ <citation type="bibtex">@ARTICLE{a1,\n+ title = {csvtk - CSV/TSV Toolkit},\n+ author = {Wei Shen},\n+ url = {https://github.com/shenwei356/csvtk}\n+ }\n+ }</citation>\n+ </citations>\n+ </xml>\n+</macros>\n\\ No newline at end of file\n' |
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| diff -r 000000000000 -r 1d4ee4308d99 replace.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/replace.xml Tue May 19 17:16:05 2020 -0400 |
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| b'@@ -0,0 +1,256 @@\n+<tool id="csvtk_replace" name="csvtk-replace" version="@VERSION@+@GALAXY_VERSION@">\n+ <description> data of selected columns by regular expression</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="requirements" />\n+ <expand macro="version_cmd" />\n+ <command detect_errors="exit_code"><![CDATA[\n+\n+###################\n+## Start Command ##\n+###################\n+csvtk replace --num-cpus "\\${GALAXY_SLOTS:-1}"\n+\n+ ## Add additional flags as specified ##\n+ #######################################\n+ $ignore_case\n+ $global_param.illegal_rows\n+ $global_param.empty_rows\n+ $global_param.header\n+ $global_param.lazy_quotes\n+\n+ ## Set Tabular input/output flag if first input is tabular ##\n+ #############################################################\n+ #if $in_1.is_of_type("tabular"):\n+ -t -T\n+ #end if\n+\n+ ## Set input files ##\n+ #####################\n+ \'$in_1\'\n+\n+ ## Specify fields to use ##\n+ ###########################\n+ -F -f \'${column_text.in_text}\'\n+ \n+ ## Specific Commands ##\n+ #######################\n+ -p \'($pattern_string)\'\n+ -r \'$replacement_string\'\n+\n+ #if $input_kv\n+ -k \'$input_kv\'\n+ #end if\n+\n+ #if $fill.how_fill == "key"\n+ -K\n+ #elif $fill.how_fill == "string"\n+ --key-miss-repl \'$fill.fill_string\'\n+ #end if\n+ \n+ ## To output ##\n+ ###############\n+ > replaced\n+\n+ ]]></command>\n+ <inputs>\n+ <expand macro="singular_input"/>\n+ <expand macro="fields_input" />\n+ <param name="pattern_string" type="text" argument="-p"\n+ label="Pattern Regex"\n+ help="Regex to search column for. Input is structured as \'(YOUR_INPUT_HERE)\' so if your regex was just a period it would look like \'(.)\' as an input.">\n+ <expand macro="text_sanitizer" />\n+ </param>\n+ <param name="replacement_string" type="text" argument="-r"\n+ label="Replacement String">\n+ <help>\n+ <![CDATA[\n+ String to replace found data. Supports capture variables and special replacement symbols.\n+\n+ - Capture Variables: $1 represents the text of the first submatch\n+ - {nr} inserts a record number starting from 1\n+ - {kv} uses corresponding value of the key (captured variable $n) of a key-value file\n+\n+ If using the special replacement symbols, the capture variable must be specified as ${1}!\n+ ]]>\n+ </help>\n+ <expand macro="text_sanitizer" />\n+ </param>\n+ <param name="input_kv" type="data" format="tsv,tabular" argument="-k"\n+ optional="true"\n+ label="Key/Value file for replacement string"\n+ help="Only specify a file if using {kv} in replacement string. The file must be tab delimited with one key/value pair per line.\n+ An example can be found in the help section below"\n+ />\n+ <conditional name="fill">\n+ <param name="how_fill" type="select" label="Fill columns that don\'t get any regex matches">\n+ <option value="no">No</option>\n+ <option value="key">Yes - Fill with Original Value</option>\n+ <option value="string">Yes - Fill with String</option>\n+ </param>\n+ <when value="no" />\n+ <when value="key" />\n+ <when value="string" >\n+ <param name="fill_string" type="text" value="NA" argument="--key-miss-repl" label="Fill string">\n+ <expand macro="text_sanitizer" />\n+ </param>\n+ </when>\n+ </conditional>\n+ <expand macro="ignore_case" />\n+ <expand macro="global_parameters" />\n+ </inputs>\n+ <outputs>\n+ <data format_source="in_1" name="replaced" from_work_dir="replaced" label=\'${in_1.name} with column ${column_text.in_text} replaced\' />\n+ </outputs>\n+ <tests>\n+ <tes'..b'>\n+ <output name="replaced" value="replace_1.csv" />\n+ </test>\n+ <test>\n+ <param name="in_1" value="replace_input.csv" />\n+ <conditional name="column_text">\n+ <param name="select" value="string" />\n+ <param name="in_text" value="2" />\n+ </conditional>\n+ <param name="pattern_string" value=".+" />\n+ <param name="replacement_string" value="{kv}" />\n+ <param name="input_kv" value="kv.txt" />\n+ <conditional name="fill">\n+ <param name="how_fill" value="key" />\n+ </conditional>\n+ <output name="replaced" value="replace_2.csv" />\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+ \n+Csvtk - Replace Help\n+--------------------\n+\n+Info\n+####\n+Csvtk-replace is a tool that uses Regular Expressions (Regex) to match data in the specified column and replace it with the replacement string.\n+Non-matched columns can be kept or filled with the Regex key or an input string\n+\n+The regex input for this tool is structured such that your regular expression **does not** need to start with with quotes or brackets. You can\n+start your expression with a `^` or just go straight into it\n+\n+For example:\n+\n+::\n+\n+ Using `.+` as an input would be used in the code as \'(.+)\'\n+\n+ Using ^(.+)$ as an input would yield an input in the code as \'(^(.+)$)\'\n+\n+.. class:: warningmark\n+\n+ Single quotes are not allowed in text inputs!\n+\n+-----\n+\n+\n+@HELP_INPUT_DATA@\n+\n+\n+Usage\n+#####\n+You can use csvtk replace to any matched regex expressions with your input replacement string.\n+\n+The replacement string has some unique properties that you can use too to better replace your data:\n+\n+- Replacement supports capture variables, like $1 which represents the text of the first submatch of the Regex\n+\n+- \\{nr} can be used to assign ascending numbers starting from 1 to each column\n+\n+- \\{kv} can be used to get the value of the key (captured variable $n) or a key-value file\n+\n+A good Regular expressions cheat sheet that you can use to help yourself build regular expressions can be found at:\n+https://regexr.com/\n+\n+**Replace Examples**\n+\n+1. Replacement with {nr} and $1\n+\n+Input file:\n+\n++---------+--------+\n+| Name | Animal |\n++=========+========+\n+| Bud | Dog |\n++---------+--------+\n+| Mittens | Cat |\n++---------+--------+\n+\n+Now if our regex was set to \'.*\' on column 2 and our replacement string was set to \'{nr}-$1\', the following output would be observed:\n+\n++---------+--------+\n+| Name | Animal |\n++=========+========+\n+| Bud | 1-Dog |\n++---------+--------+\n+| Mittens | 2-Cat |\n++---------+--------+\n+\n+---------------\n+\n+2. Replacement with {kv} file\n+\n+Suppose you set up a key-value TAB separated file that looked as such:\n+\n+::\n+\n+ Key Value\n+ Dog Big\n+ Cat Small\n+\n+And had a similar input file:\n+\n++---------+--------+\n+| Name | Animal |\n++=========+========+\n+| Bud | Dog |\n++---------+--------+\n+| Mittens | Cat |\n++---------+--------+\n+| Fuzzy | Gerbil |\n++---------+--------+\n+\n+Now if the regex was \'.*\' on column 2 with the replacement string as \'{kv}\'. Your output would look as such with \'No\' fill specified:\n+\n++---------+--------+\n+| Name | Animal |\n++=========+========+\n+| Bud | Big |\n++---------+--------+\n+| Mittens | Small |\n++---------+--------+\n+| Fuzzy | |\n++---------+--------+\n+\n+If you wanted to fill the blank cell you could set it to either:\n+\n+- String - the string you input (ex. \'NA\') would fill up the blank cell.\n+\n+- Original value - would change the blank cell to \'Gerbil\'\n+\n+----\n+\n+If your having trouble with the regular expressions, please play around with a builder, there are many others online \n+and they are great resources to improve your regex statements or test them before use!\n+\n+----\n+\n+@HELP_END_STATEMENT@\n+\n+\n+ ]]></help>\n+ <expand macro="citations" />\n+</tool>\n\\ No newline at end of file\n' |
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| diff -r 000000000000 -r 1d4ee4308d99 test-data/Animals_More.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Animals_More.csv Tue May 19 17:16:05 2020 -0400 |
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| @@ -0,0 +1,10 @@ +Name,Animal,Random_Number +Spots,Dog,1 +Fred,Dog,5 +Mittens,Cat,16 +Slippers,Cat,11 +Gravy,Cat,6 +Stripes,Zebra,7 +Muffin,Cat,7 +Earl,Dog,2 +Sir-Wags-A-Lot,Dog,44 |
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| diff -r 000000000000 -r 1d4ee4308d99 test-data/XY_converted.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/XY_converted.csv Tue May 19 17:16:05 2020 -0400 |
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| @@ -0,0 +1,12 @@ +X,Y +1,2 +2,4 +4,8 +8,16 +16,32 +32,64 +64,128 +128,256 +256,512 +1024,2048 +2048,5096 |
| b |
| diff -r 000000000000 -r 1d4ee4308d99 test-data/XY_converted.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/XY_converted.tsv Tue May 19 17:16:05 2020 -0400 |
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| @@ -0,0 +1,12 @@ +X Y +1 2 +2 4 +4 8 +8 16 +16 32 +32 64 +64 128 +128 256 +256 512 +1024 2048 +2048 5096 |
| b |
| diff -r 000000000000 -r 1d4ee4308d99 test-data/XY_with_break.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/XY_with_break.csv Tue May 19 17:16:05 2020 -0400 |
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| @@ -0,0 +1,13 @@ +X,Y +1,2 +2,4 +4,8 +8,16 +16,32 +32,64 +64,128 +128,256 +256,512 +, +1024,2048 +2048,5096 |
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| diff -r 000000000000 -r 1d4ee4308d99 test-data/XY_with_break.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/XY_with_break.tabular Tue May 19 17:16:05 2020 -0400 |
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| @@ -0,0 +1,13 @@ +X Y +1 2 +2 4 +4 8 +8 16 +16 32 +32 64 +64 128 +128 256 +256 512 + +1024 2048 +2048 5096 |
| b |
| diff -r 000000000000 -r 1d4ee4308d99 test-data/another.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/another.csv Tue May 19 17:16:05 2020 -0400 |
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| @@ -0,0 +1,4 @@ +Name,Food,Age +Joe,Beets,33 +Steven,Eggplant,36 +Jacob,Kale,59 \ No newline at end of file |
| b |
| diff -r 000000000000 -r 1d4ee4308d99 test-data/awk_mutate_input.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/awk_mutate_input.csv Tue May 19 17:16:05 2020 -0400 |
| b |
| @@ -0,0 +1,4 @@ +Culture Label,Cell Count,Dilution +ECo-1,2523,1000 +LPn-1,100,1000000 +LPn-2,4,1000 |
| b |
| diff -r 000000000000 -r 1d4ee4308d99 test-data/awk_mutate_output.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/awk_mutate_output.csv Tue May 19 17:16:05 2020 -0400 |
| b |
| @@ -0,0 +1,4 @@ +Culture Label,Cell Count,Dilution,CFU/ml +ECo-1,2523,1000,2523000 +LPn-1,100,1000000,100000000 +LPn-2,4,1000,4000 |
| b |
| diff -r 000000000000 -r 1d4ee4308d99 test-data/blood_type.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blood_type.tsv Tue May 19 17:16:05 2020 -0400 |
| b |
| @@ -0,0 +1,11 @@ +Name Blood_Type Favourite_Colour Height +Darian AB Blue 175cm +Fred AB- Orange 185cm +Jacob AB Blue 160cm +Adrian O Blue 2000cm +Tim O- Green 20cm +Matthew O Green 140cm +Patrick O Green 1cm +Chester O Blue 22cm +Kim B Teal 11cm +Sarah A Blue 123cm |
| b |
| diff -r 000000000000 -r 1d4ee4308d99 test-data/collapsed.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/collapsed.tsv Tue May 19 17:16:05 2020 -0400 |
| b |
| @@ -0,0 +1,7 @@ +Blood_Type Name +AB- Fred +AB Darian; Jacob +O- Tim +O Adrian; Matthew; Patrick; Chester +B Kim +A Sarah |
| b |
| diff -r 000000000000 -r 1d4ee4308d99 test-data/concat_1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/concat_1.csv Tue May 19 17:16:05 2020 -0400 |
| b |
| @@ -0,0 +1,11 @@ +Name,Colour,Food +Eric,Blue,Apples +Darian,Blue,Pancakes +Daniel,Red,Apples +Emily,Blue,Apples +Fred,-,- +Adrian,-,- +Steven,-,- +Joe,-,Beets +Steven,-,Eggplant +Jacob,-,Kale |
| b |
| diff -r 000000000000 -r 1d4ee4308d99 test-data/concat_2.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/concat_2.csv Tue May 19 17:16:05 2020 -0400 |
| b |
| @@ -0,0 +1,11 @@ +Name,Colour,Food +Eric,Blue,Apples +Darian,Blue,Pancakes +Daniel,Red,Apples +Emily,Blue,Apples +Fred,, +Adrian,, +Steven,, +Joe,,Beets +Steven,,Eggplant +Jacob,,Kale |
| b |
| diff -r 000000000000 -r 1d4ee4308d99 test-data/corr_1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/corr_1.csv Tue May 19 17:16:05 2020 -0400 |
| b |
| @@ -0,0 +1,1 @@ +X,Y,0.9960 |
| b |
| diff -r 000000000000 -r 1d4ee4308d99 test-data/corr_2.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/corr_2.tsv Tue May 19 17:16:05 2020 -0400 |
| b |
| @@ -0,0 +1,1 @@ +X Y 0.9997 |
| b |
| diff -r 000000000000 -r 1d4ee4308d99 test-data/csv-bob.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/csv-bob.csv Tue May 19 17:16:05 2020 -0400 |
| b |
| @@ -0,0 +1,2 @@ +Person,Favourite Food,Favourite Colour,Height,BloodType +Bob,Protein,All of them,250cm,O- |
| b |
| diff -r 000000000000 -r 1d4ee4308d99 test-data/csv-darian.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/csv-darian.csv Tue May 19 17:16:05 2020 -0400 |
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| @@ -0,0 +1,2 @@ +Person,Favourite Food,Favourite Colour,Height,BloodType +Darian,Potatos,Blue,175cm,O |
| b |
| diff -r 000000000000 -r 1d4ee4308d99 test-data/csv-jack.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/csv-jack.csv Tue May 19 17:16:05 2020 -0400 |
| b |
| @@ -0,0 +1,2 @@ +Person,Favourite Food,Favourite Colour,Height,BloodType +Jack,Pineapple,Off White,165cm,O |
| b |
| diff -r 000000000000 -r 1d4ee4308d99 test-data/csv.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/csv.csv Tue May 19 17:16:05 2020 -0400 |
| b |
| @@ -0,0 +1,4 @@ +Person,Favourite Food,Favourite Colour,Height,BloodType +Jack,Pineapple,Off White,165cm,O +Bob,Protein,All of them,250cm,O- +Darian,Potatos,Blue,175cm,O |
| b |
| diff -r 000000000000 -r 1d4ee4308d99 test-data/cut_1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cut_1.csv Tue May 19 17:16:05 2020 -0400 |
| b |
| @@ -0,0 +1,33 @@ +Length,GC Content +100,50.00 +100,50.05 +100,49.95 +110,50.60 +105,50.50 +101,49.05 +99,49.95 +95,50.95 +100,50.00 +100,50.00 +90,66.00 +100,66.60 +100,65.05 +101,65.95 +101,65.55 +99,66.00 +95,66.05 +100,66.55 +105,65.55 +100,65.55 +110,66.55 +110,70.00 +100,70.00 +90,45.65 +99,45.60 +99,45.50 +95,45.20 +95,45.55 +100,45.55 +100,45.20 +100,45.55 +100,45.50 |
| b |
| diff -r 000000000000 -r 1d4ee4308d99 test-data/cut_2.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cut_2.csv Tue May 19 17:16:05 2020 -0400 |
| b |
| @@ -0,0 +1,33 @@ +Group,GC Content +A,50.00 +A,50.05 +A,49.95 +A,50.60 +A,50.50 +A,49.05 +A,49.95 +A,50.95 +A,50.00 +A,50.00 +B,66.00 +B,66.60 +B,65.05 +B,65.95 +B,65.55 +B,66.00 +B,66.05 +B,66.55 +B,65.55 +B,65.55 +B,66.55 +C,70.00 +C,70.00 +D,45.65 +D,45.60 +D,45.50 +D,45.20 +D,45.55 +D,45.55 +D,45.20 +D,45.55 +D,45.50 |
| b |
| diff -r 000000000000 -r 1d4ee4308d99 test-data/data.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/data.csv Tue May 19 17:16:05 2020 -0400 |
| b |
| @@ -0,0 +1,4 @@ +Person,Height,Sport,Job +Fred,140cm,Diving,Accountant +Darian,175cm,Running,Student +Jake,188cm,Shotput,Moving Heavy Objects |
| b |
| diff -r 000000000000 -r 1d4ee4308d99 test-data/filtered.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/filtered.tsv Tue May 19 17:16:05 2020 -0400 |
| b |
| @@ -0,0 +1,4 @@ +Blood_Type Favourite_Colour frequency +AB Blue 2 +O Green 2 +O Blue 2 |
| b |
| diff -r 000000000000 -r 1d4ee4308d99 test-data/frequency.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/frequency.tsv Tue May 19 17:16:05 2020 -0400 |
| b |
| @@ -0,0 +1,8 @@ +Blood_Type Favourite_Colour frequency +AB- Orange 1 +AB Blue 2 +O- Green 1 +O Green 2 +O Blue 2 +B Teal 1 +A Blue 1 |
| b |
| diff -r 000000000000 -r 1d4ee4308d99 test-data/gathered.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gathered.csv Tue May 19 17:16:05 2020 -0400 |
| b |
| @@ -0,0 +1,4 @@ +Favourite Food,Favourite Colour,Height,BloodType,1,2 +Pineapple,Off White,165cm,O,Person,Jack +Protein,All of them,250cm,O-,Person,Bob +Potatos,Blue,175cm,O,Person,Darian |
| b |
| diff -r 000000000000 -r 1d4ee4308d99 test-data/illegal.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/illegal.csv Tue May 19 17:16:05 2020 -0400 |
| b |
| @@ -0,0 +1,6 @@ +Test,A,B,C +D,,S,C +F,F,F,F +F,F,F, +TT,TT,TT,TT +Agh,Ol,As,TT \ No newline at end of file |
| b |
| diff -r 000000000000 -r 1d4ee4308d99 test-data/illegal_collapse.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/illegal_collapse.csv Tue May 19 17:16:05 2020 -0400 |
| b |
| @@ -0,0 +1,5 @@ +C,Test +C,D +F,F +,F +TT,TT; Agh |
| b |
| diff -r 000000000000 -r 1d4ee4308d99 test-data/joined.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/joined.csv Tue May 19 17:16:05 2020 -0400 |
| b |
| @@ -0,0 +1,2 @@ +Person,Favourite Food,Favourite Colour,Height,BloodType,Height,Sport,Job +Darian,Potatos,Blue,175cm,O,175cm,Running,Student |
| b |
| diff -r 000000000000 -r 1d4ee4308d99 test-data/joined_filled.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/joined_filled.csv Tue May 19 17:16:05 2020 -0400 |
| b |
| @@ -0,0 +1,6 @@ +Person,Favourite Food,Favourite Colour,Height,BloodType,Height,Sport,Job +Jack,Pineapple,Off White,165cm,O,a,a,a +Bob,Protein,All of them,250cm,O-,a,a,a +Darian,Potatos,Blue,175cm,O,175cm,Running,Student +Fred,a,a,a,a,140cm,Diving,Accountant +Jake,a,a,a,a,188cm,Shotput,Moving Heavy Objects |
| b |
| diff -r 000000000000 -r 1d4ee4308d99 test-data/kv.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/kv.txt Tue May 19 17:16:05 2020 -0400 |
| b |
| @@ -0,0 +1,3 @@ +Key Value +Dog Big +Cat Small \ No newline at end of file |
| b |
| diff -r 000000000000 -r 1d4ee4308d99 test-data/line_all_param.png |
| b |
| Binary file test-data/line_all_param.png has changed |
| b |
| diff -r 000000000000 -r 1d4ee4308d99 test-data/mutate_removed.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mutate_removed.tsv Tue May 19 17:16:05 2020 -0400 |
| b |
| @@ -0,0 +1,11 @@ +Blood_Type Favourite_Colour Height new_column +AB Blue 175cm Darian +AB- Orange 185cm +AB Blue 160cm +O Blue 2000cm +O- Green 20cm +O Green 140cm +O Green 1cm +O Blue 22cm +B Teal 11cm +A Blue 123cm |
| b |
| diff -r 000000000000 -r 1d4ee4308d99 test-data/mutated.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mutated.tsv Tue May 19 17:16:05 2020 -0400 |
| b |
| @@ -0,0 +1,11 @@ +Name Blood_Type Favourite_Colour Height new_column +Darian AB Blue 175cm Darian +Fred AB- Orange 185cm Fred +Jacob AB Blue 160cm Jacob +Adrian O Blue 2000cm Adrian +Tim O- Green 20cm Tim +Matthew O Green 140cm Matthew +Patrick O Green 1cm Patrick +Chester O Blue 22cm Chester +Kim B Teal 11cm Kim +Sarah A Blue 123cm Sarah |
| b |
| diff -r 000000000000 -r 1d4ee4308d99 test-data/other.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/other.csv Tue May 19 17:16:05 2020 -0400 |
| b |
| @@ -0,0 +1,4 @@ +Name,Sport,Job +Fred,Volleyball,Molecular Biologist +Adrian,Basketball,Computational Biologist +Steven,Football,Microbiologist \ No newline at end of file |
| b |
| diff -r 000000000000 -r 1d4ee4308d99 test-data/plot.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/plot.csv Tue May 19 17:16:05 2020 -0400 |
| b |
| @@ -0,0 +1,33 @@ +Group,Length,GC Content +A,100,50.00 +A,100,50.05 +A,100,49.95 +A,110,50.60 +A,105,50.50 +A,101,49.05 +A,99,49.95 +A,95,50.95 +A,100,50.00 +A,100,50.00 +B,90,66.00 +B,100,66.60 +B,100,65.05 +B,101,65.95 +B,101,65.55 +B,99,66.00 +B,95,66.05 +B,100,66.55 +B,105,65.55 +B,100,65.55 +B,110,66.55 +C,110,70.00 +C,100,70.00 +D,90,45.65 +D,99,45.60 +D,99,45.50 +D,95,45.20 +D,95,45.55 +D,100,45.55 +D,100,45.20 +D,100,45.55 +D,100,45.50 \ No newline at end of file |
| b |
| diff -r 000000000000 -r 1d4ee4308d99 test-data/plot.png |
| b |
| Binary file test-data/plot.png has changed |
| b |
| diff -r 000000000000 -r 1d4ee4308d99 test-data/plot_box.png |
| b |
| Binary file test-data/plot_box.png has changed |
| b |
| diff -r 000000000000 -r 1d4ee4308d99 test-data/plot_scatter.png |
| b |
| Binary file test-data/plot_scatter.png has changed |
| b |
| diff -r 000000000000 -r 1d4ee4308d99 test-data/replace_1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/replace_1.csv Tue May 19 17:16:05 2020 -0400 |
| b |
| @@ -0,0 +1,4 @@ +Name,Animal +Shirley,1-Dog +Mittens,2-Cat +Fuzzy,3-Chinchilla |
| b |
| diff -r 000000000000 -r 1d4ee4308d99 test-data/replace_2.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/replace_2.csv Tue May 19 17:16:05 2020 -0400 |
| b |
| @@ -0,0 +1,4 @@ +Name,Animal +Shirley,Big +Mittens,Small +Fuzzy,Chinchilla |
| b |
| diff -r 000000000000 -r 1d4ee4308d99 test-data/replace_input.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/replace_input.csv Tue May 19 17:16:05 2020 -0400 |
| b |
| @@ -0,0 +1,4 @@ +Name,Animal +Shirley,Dog +Mittens,Cat +Fuzzy,Chinchilla |
| b |
| diff -r 000000000000 -r 1d4ee4308d99 test-data/sampled_1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sampled_1.csv Tue May 19 17:16:05 2020 -0400 |
| b |
| @@ -0,0 +1,16 @@ +Group,Length,GC Content +A,100,50.00 +A,101,49.05 +A,100,50.00 +A,100,50.00 +B,90,66.00 +B,100,66.60 +B,101,65.55 +B,99,66.00 +B,105,65.55 +D,90,45.65 +D,99,45.60 +D,99,45.50 +D,95,45.20 +D,95,45.55 +D,100,45.20 |
| b |
| diff -r 000000000000 -r 1d4ee4308d99 test-data/sampled_2.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sampled_2.csv Tue May 19 17:16:05 2020 -0400 |
| b |
| @@ -0,0 +1,25 @@ +n,Group,Length,GC Content +1,A,100,50.00 +4,A,110,50.60 +5,A,105,50.50 +6,A,101,49.05 +9,A,100,50.00 +10,A,100,50.00 +11,B,90,66.00 +12,B,100,66.60 +13,B,100,65.05 +14,B,101,65.95 +15,B,101,65.55 +16,B,99,66.00 +19,B,105,65.55 +20,B,100,65.55 +22,C,110,70.00 +24,D,90,45.65 +25,D,99,45.60 +26,D,99,45.50 +27,D,95,45.20 +28,D,95,45.55 +29,D,100,45.55 +30,D,100,45.20 +31,D,100,45.55 +32,D,100,45.50 |
| b |
| diff -r 000000000000 -r 1d4ee4308d99 test-data/separated_1.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/separated_1.tsv Tue May 19 17:16:05 2020 -0400 |
| b |
| @@ -0,0 +1,7 @@ +Blood_Type 1 2 +AB- Fred NA +AB Darian Jacob +O- Tim NA +O Adrian Matthew +B Kim NA +A Sarah NA |
| b |
| diff -r 000000000000 -r 1d4ee4308d99 test-data/separated_2.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/separated_2.tsv Tue May 19 17:16:05 2020 -0400 |
| b |
| @@ -0,0 +1,7 @@ +Blood_Type Name 1 2 +AB- Fred Fred N/A +AB Darian; Jacob Darian Jacob +O- Tim Tim N/A +O Adrian; Matthew; Patrick; Chester Adrian Matthew; Patrick; Chester +B Kim Kim N/A +A Sarah Sarah N/A |
| b |
| diff -r 000000000000 -r 1d4ee4308d99 test-data/sort_order.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sort_order.txt Tue May 19 17:16:05 2020 -0400 |
| b |
| @@ -0,0 +1,3 @@ +Zebra +Cat +Dog |
| b |
| diff -r 000000000000 -r 1d4ee4308d99 test-data/sorted_1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sorted_1.csv Tue May 19 17:16:05 2020 -0400 |
| b |
| @@ -0,0 +1,10 @@ +Name,Animal,Random_Number +Stripes,Zebra,7 +Mittens,Cat,16 +Slippers,Cat,11 +Muffin,Cat,7 +Gravy,Cat,6 +Sir-Wags-A-Lot,Dog,44 +Fred,Dog,5 +Earl,Dog,2 +Spots,Dog,1 |
| b |
| diff -r 000000000000 -r 1d4ee4308d99 test-data/test.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.csv Tue May 19 17:16:05 2020 -0400 |
| b |
| @@ -0,0 +1,5 @@ +Name,Colour,Food +Eric,Blue,Apples +Darian,Blue,Pancakes +Daniel,Red,Apples +Emily,Blue,Apples \ No newline at end of file |
| b |
| diff -r 000000000000 -r 1d4ee4308d99 test-data/uniq.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/uniq.tsv Tue May 19 17:16:05 2020 -0400 |
| b |
| @@ -0,0 +1,8 @@ +Name Blood_Type Favourite_Colour Height +Darian AB Blue 175cm +Fred AB- Orange 185cm +Adrian O Blue 2000cm +Tim O- Green 20cm +Matthew O Green 140cm +Kim B Teal 11cm +Sarah A Blue 123cm |
