Mercurial > repos > cpt > cpt_psm_plotter
diff cpt_psm_1_plot.xml @ 1:8691c1c61a8e draft default tip
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
| author | cpt |
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| date | Mon, 05 Jun 2023 02:48:47 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cpt_psm_1_plot.xml Mon Jun 05 02:48:47 2023 +0000 @@ -0,0 +1,163 @@ +<tool id="PSM.Plot" name="PSM Plotter" version="1.94.2"> + <description>plots data from PSM Prep</description> + <version_command>perl cpt_psm_1_plot.pl --version</version_command> + <stdio> + <exit_code range="1:" level="fatal"/> + </stdio> + <requirements> + <requirement type="package" version="5.22.1">perl</requirement> + <requirement type="package">perl-bioperl</requirement> + <requirement type="package">perl-moose</requirement> + <requirement type="package">perl-ipc-run</requirement> + <requirement type="package">perl-getopt-long-descriptive</requirement> + </requirements> + <command detect_errors="aggressive"><![CDATA[ +perl -Mlib='$__tool_directory__/lib' '$__tool_directory__/cpt_psm_1_plot.pl' +--galaxy +--outfile_supporting '$__new_file_path__' +--file "${file}" + +--user_ordering "${user_ordering}" + +#if $percent_filled and $percent_filled is not "None": +--percent_filled "${percent_filled}" +#end if + +#if $ig_dist and $ig_dist is not "None": +--ig_dist "${ig_dist}" +#end if + +#if $stroke_thickness and $stroke_thickness is not "None": +--stroke_thickness "${stroke_thickness}" +#end if + +#if $every_nth and $every_nth is not "None": +--every_nth "${every_nth}" +#end if + +#if $evalue and $evalue is not "None": +--evalue "${evalue}" +#end if + +#if $dice and $dice is not "None": +--dice "${dice}" +#end if + +#if $mismatch and $mismatch is not "None": +--mismatch "${mismatch}" +#end if + +#if $gap_penalty and $gap_penalty is not "None": +--gap_penalty "${gap_penalty}" +#end if + +#if $match and $match is not "None": +--match "${match}" +#end if + +--output_circos_confs "${output_circos_confs}" + +--output_circos_confs_files_path "${output_circos_confs.files_path}" + +--output_circos_confs_format "${output_circos_confs_format}" + +--output_circos_confs_id "${output_circos_confs.id}" + +]]></command> + <inputs> + <param name="file" help="PSM2 Data File" optional="False" label="file" type="data"/> + <param name="user_ordering" help="List of genome IDs used in the analysis, can be comma/space/newline separated." optional="False" label="user_ordering" type="text"/> + <param min="0.1" value="0.8" max="1.0" name="percent_filled" optional="True" help="Percentage of a whole block that an individual gene is" type="float" label="percent_filled"/> + <param value="100" name="ig_dist" help="Maximum length of links between genome comparisons" optional="True" label="ig_dist" type="integer"/> + <param min="1" value="2" max="10" name="stroke_thickness" optional="True" help="Thickness of inter-genome links" type="integer" label="stroke_thickness"/> + <param value="20" name="every_nth" optional="True" help="Plot every Nth gene a modified version of the main color for that genome" label="every_nth" type="integer"/> + <param value="0.0001" name="evalue" optional="True" help="Evalue cutoff" label="evalue" type="float"/> + <param value="50" name="dice" optional="True" help="Dice cutoff" label="dice" type="float"/> + <param value="-0.1" name="mismatch" optional="True" help="Mismatch Score" label="mismatch" type="float"/> + <param value="0.0" name="gap_penalty" optional="True" help="Gap Penalty" label="gap_penalty" type="float"/> + <param value="5" name="match" optional="True" help="Match Score" label="match" type="float"/> + <param name="output_circos_confs_format" help="Output Circos Conf Object" optional="False" label="Format of output_circos_confs" type="select"> + <option value="zip">zip</option> + </param> + </inputs> + <outputs> + <data name="output_circos_confs" format="tar.gz"> + <change_format> + <when input="output_circos_confs_format" value="tar.gz" format="tar.gz"/> + <when input="output_circos_confs_format" value="zip" format="zip"/> + <when input="output_circos_confs_format" value="tar" format="tar"/> + </change_format> + </data> + </outputs> + <help>NAME +==== + +PSM Plotter + +DESCRIPTION +=========== + +Following the execution of the PSM Prep tool, this tool plots a subset +of those genomes as ciruclar tracks with protein-protein relationships +plotted as links between the boxes representing proteins. + +IMPORTANT PARAMETERS +-------------------- + +- ``user_ordering`` + + This parameter controls the order in which genomes are aligned and + then plotted. This MUST contain (comma/space) separated values + listing the order (outside to in) in which you want your genomes to + appear. In this field, type the name of each genome. The name can be + found on the first line of the file under "LOCUS NC\_00000001", where + NC\_00000001 would be the genome's name. + +- ``evalue``, ``dice`` + + Adjusting these parameters will affect which links are plotted. Links + are heatmapped into bins based on dice score as that is the easiest + measure to work with, and scales nicely from 0 to 100. For example, a + link with a dice score of 20-29 would be plotted as 20% black + (grey20), whereas a dice score of 90+ would be plotted as solid black + +- ``mismatch``, ``gap_penalty``, ``match`` + + These parameters control the Needleman-Wunsch Multiple Sequence + Alignment library's scoring scheme. Mismatch scores are generally + negative and discourage unrelated proteins from being plotted in a + line together. Match scores encourage related proteins to line up. + Gap penalty is set at zero as we generally prefer gaps to mismatches + in this tool; phage genomes are small and gaps are "cheap" to use, + whereas mismatches can sometimes give an incorrect impression of + relatedness. That said, how your plots look is completely up to you + and we encourage experimentation! + +- ``every_nth`` + + Every Nth gene in a genome will be plotted a slightly different + color. + +Why Can't I Control Colors? +--------------------------- + +:: + + Brewer colors compose Brewer palettes which have been manually defined by + Cynthia Brewer for their perceptual properties. + + http://circos.ca/tutorials/lessons/configuration/colors/ + +Color palette choice is very important to creating an attractive and +easy to read graphic. In the words of Dr. Krzywinski, `Color palettes +matter <http://mkweb.bcgsc.ca/jclub/biovis/brewer/colorpalettes.pdf>`__. +Humans selecting from an RGB/HSV color palette tend to make poor +choices, so we've removed the option in lieu of using the very +attractive `Brewer Palettes <http://colorbrewer2.org/>`__. Specifically, +I've selected the 8 class qualtitative "Accent" color set, which has +produced some very nice maps. If you would like the option of selecting +amongst the other 8-class qualitative color sets, please file a bug +report and let me know. +</help> + <tests/> +</tool>