Mercurial > repos > nml > csvtk_cut
diff macros.xml @ 0:5b5330a8dfac draft default tip
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
| author | nml |
|---|---|
| date | Tue, 19 May 2020 17:09:36 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue May 19 17:09:36 2020 -0400 @@ -0,0 +1,337 @@ +<macros> + <token name="@VERSION@">0.20.0</token> + <token name="@GALAXY_VERSION@">galaxy0</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@VERSION@">csvtk</requirement> + </requirements> + </xml> + <xml name="version_cmd"> + <version_command>csvtk version</version_command> + </xml> + <xml name="text_sanitizer"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + </valid> + </sanitizer> + </xml> + <xml name="multi_input"> + <param type="data" name="in_1" format="csv,tabular" + multiple="true" optional="false" + label="Specify TSV or CSV file inputs" + 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!" + /> + </xml> + <xml name="singular_input"> + <param type="data" name="in_1" format="csv,tabular" + multiple="false" optional="false" + label="Specify an input TSV or CSV file" + help="Input a TSV or CSV file to work on" + /> + </xml> + <xml name="ignore_case"> + <param type="boolean" name="ignore_case" + falsevalue="" truevalue="-i" + checked="false" + argument="-i" + label="Ignore cell case?" + help="ABC == abc" + /> + </xml> + <xml name="global_parameters"> + <section name="global_param" title="csvtk Global Parameters" expanded="false"> + <param type="boolean" name="header" + falsevalue="-H" truevalue="" + checked="true" + argument="-H" + label="Input file has a header line" + /> + <param type="boolean" name="illegal_rows" + falsevalue="" truevalue="-I" + checked="false" + argument="-I" + label="Ignore illegal rows" + help="Use if file has illegal rows as defined in the help section" + /> + <param type="boolean" name="empty_rows" + falsevalue="" truevalue="-E" + checked="false" + argument="-E" + label="Ignore empty rows" + help="Ignore rows with no data (only needed if input has empty rows)" + /> + <param type="boolean" name="lazy_quotes" + falsevalue="" truevalue="-l" + checked="false" + argument="-l" + label="File has Lazy quotes" + 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" + /> + </section> + </xml> + <xml name="fields_input"> + <conditional name="column_text" > + <param type="select" name="select" label="Select input column(s) based on" argument="-F -f"> + <option value="string">Column Name(s)</option> + <option value="column">Column Number(s)</option> + </param> + <when value="column"> + <param type="data_column" name="in_text" + data_ref="in_1" + multiple="true" + label="Input column number(s)" + help="Select column(s) to use for analysis" + /> + </when> + <when value="string"> + <param type="text" name="in_text" + optional="false" + label="Input column name(s)" + help="Multiple columns can be given if separated by a ' , '. + Column numbers can be given too - ex. '1,2' will target columns 1 and 2. + Please see the help section below for more detailed info"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + </valid> + </sanitizer> + </param> + </when> + </conditional> + </xml> + <xml name="singular_fields_input"> + <conditional name="column_text" > + <param type="select" name="select" label="Select input column based on" argument="-f"> + <option value="string">Column Name</option> + <option value="column">Column Number</option> + </param> + <when value="column"> + <param type="data_column" name="in_text" + data_ref="in_1" + multiple="false" + label="Input column number" + help="Select column to use for analysis" + /> + </when> + <when value="string"> + <param type="text" name="in_text" + optional="false" + label="Input column name" + help="Input column name or number ex. 'Length' or '1'. + Please see the help section below for more detailed info"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + </valid> + </sanitizer> + </param> + </when> + </conditional> + </xml> + <xml name="plot_field"> + <conditional name="column_text" > + <param type="select" name="select" label="Select input data column based on" argument="-f"> + <option value="string">Column Name</option> + <option value="column">Column Number</option> + </param> + <when value="column"> + <param type="data_column" name="in_text" + data_ref="in_1" + multiple="false" + label="Input data column number" + /> + </when> + <when value="string"> + <param type="text" name="in_text" + optional="false" + label="Input data column name" + help="Can use column name or column number"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + </valid> + </sanitizer> + </param> + </when> + </conditional> + </xml> + <xml name="groups_input"> + <conditional name="group_field" > + <param type="select" name="select_group" label="Select column to group data" argument="-g" optional="false" help="Specify a single column that is used to create data groups. An example is shown in the help section"> + <option value="none">None</option> + <option value="string">Column Name</option> + <option value="column">Column Number</option> + </param> + <when value="none" /> + <when value="column"> + <param type="data_column" name="in_text" + data_ref="in_1" + multiple="false" + label="Group by column number" + /> + </when> + <when value="string"> + <param type="text" name="in_text" + optional="false" + label="Group by column name" + help="Can use column name or number"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + </valid> + </sanitizer> + </param> + </when> + </conditional> + </xml> + <xml name="global_plot_parameters"> + <section name="plot_parameters" title="Advanced Optional Plot Parameters" expanded="false"> + <param type="float" name="figure_height" + argument="--height" + optional="true" + label="Figure Height (Default 4.5)" + /> + <param type="float" name="figure_width" + argument="--width" + optional="true" + label="Figure Width (Default 1.5)" + /> + <param type="float" name="tick_width" + argument="--tick-width" + optional="true" + label="Axis Tick Width (Default 1.5)" + /> + <param type="text" name="title" + argument="--title" + optional="true" + label="Specify Figure Title"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + </valid> + </sanitizer> + </param> + <param type="text" name="x_label" + argument="--xlab" + optional="true" + label="Specify X-axis label"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + </valid> + </sanitizer> + </param> + <param type="float" name="min_x" + argument="--x-min" + optional="true" + label="Minimum value of X-axis (float)" + /> + <param type="float" name="max_x" + argument="--x-max" + optional="true" + label="Maximum value of X-axis (float)" + /> + <param type="text" name="y_label" + argument="--ylab" + optional="true" + label="Specify Y-axis label"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + </valid> + </sanitizer> + </param> + <param type="float" name="min_y" + argument="--y-min" + optional="true" + label="Minimum value of Y-axis (float)" + /> + <param type="float" name="max_y" + argument="--y-max" + optional="true" + label="Maximum value of Y-axis (float)" + /> + </section> + </xml> + <token name="@HELP_COLUMNS@"> +Column Name Input Help +###################### + +- Multiple names can be given if separated by a ' , '. + + - ex. 'ID,Organism' would target the columns named ID and Organism for the function + +- Column names are case SeNsitive + +- Column numbers can also be given: + + -ex. '1,2,3' or '1-3' for inputting columns 1-3. + +- You can also specify all but unwanted column(s) with a ' - '. + + - ex. '-ID' would target all columns but the ID column + +---- + </token> + <token name="@HELP_INPUT_DATA@"> +Input Data +########## + +:: + + **Limitations of Input Data** + + 1. The CSV parser requires all the lines have same number of fields/columns. + If your file has illegal rows, set the "Illegal Rows" parameter to "Yes" to pass your data through + Even lines with spaces will cause error. + Example bad table below. + + 2. By default, csvtk thinks files have header rows. If your file does not, set global parameter + "Has Header Row" to "No" + + 3. Column names should be unique and are case sensitive! + + 4. Lines starting with "#" or "$" will be ignored, if in the header row + + 5. If " exists in tab-delimited files, set Lazy quotes global parameter to "Yes" + +Example bad table: + ++--------+--------+--------+--------+ +| Head 1 | Head 2 | Head 3 | Head 3 | ++========+========+========+========+ +| 1 | 2 | 3 | | ++--------+--------+--------+--------+ +| this | will | | break | ++--------+--------+--------+--------+ + +Bad tables may work if both the "Ignore Illegal Rows" and "Ignore Empty Rows" global parameters are set to "Yes", +But there is no guarentee of that! + +---- + </token> + <token name="@HELP_END_STATEMENT@"> +More Information +################ +For information from the creators of csvtk, please visit their site at: https://bioinf.shenwei.me/csvtk/ + +Although be aware that some features may not be available and some small changes were made to work with Galaxy. + +**Notable changes from their documentation:** + +- Cannot specify multiple file header names (IE cannot use "name;username" as a valid column match) + +- No single quotes / apostrophes allowed in text inputs + </token> + <xml name="citations"> + <citations> + <citation type="bibtex">@ARTICLE{a1, + title = {csvtk - CSV/TSV Toolkit}, + author = {Wei Shen}, + url = {https://github.com/shenwei356/csvtk} + } + }</citation> + </citations> + </xml> +</macros> \ No newline at end of file