Mercurial > repos > iuc > pygenometracks
diff macros.xml @ 2:c171f2b7d76e draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
| author | iuc |
|---|---|
| date | Fri, 23 Aug 2019 07:24:20 -0400 |
| parents | 2074627b0f83 |
| children | c237ba772225 |
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--- a/macros.xml Mon Jul 02 19:32:13 2018 -0400 +++ b/macros.xml Fri Aug 23 07:24:20 2019 -0400 @@ -1,12 +1,13 @@ <macros> <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token> - <token name="@WRAPPER_VERSION@">2.0</token> + <token name="@WRAPPER_VERSION@">3.1</token> <xml name="requirements"> <requirements> <requirement type="package" version="@WRAPPER_VERSION@">pygenometracks</requirement> + <!--<requirement type="package" version="3.7">python</requirement>--> <yield /> </requirements> - <version_command>@BINARY@ --version</version_command> + <version_command><![CDATA[@BINARY@ --version | tail -n 1 ]]></version_command> </xml> <xml name="citations"> @@ -188,6 +189,9 @@ <xml name="track_input_bed_macro"> <param name="track_input_bed" type="data" format="bed" label="Track file bed format" multiple='True'/> </xml> + <xml name="track_input_bed_gtf_macro"> + <param name="track_input_bed" type="data" format="bed,gtf" label="Track file bed or gtf format" multiple='True'/> + </xml> <xml name="track_input_bed_single_macro"> <param name="track_input_bed_single" type="data" format="bed" label="Track file bed format"/> </xml> @@ -207,4 +211,219 @@ <param name="spacer_height" type="float" value="" optional="True" label="Include spacer at the end of the track" help="Height of the spacer." /> </xml> + <xml name="inverted_macro"> + <param name="invert_orientation" type="boolean" truevalue="yes" falsevalue="no" checked="false" + label="Invert the track" /> + </xml> + <xml name="color_bed_macro"> + <conditional name="color_bed"> + <param name="color_bed_select" type="select" label="Use color:"> + <option value="manually" selected="True">manually</option> + <option value="bed_rgb">From the 9th field</option> + <option value="colormap">From the 5th field (score)</option> + </param> + <when value="manually"> + <param name="color" type="color" value="#000000" label="Color of track" optional="True" /> + </when> + <when value="bed_rgb" /> + <when value="colormap"> + <param name="color" type="select" label="Color map to use for the scores" help=" Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html"> + <option value="RdYlBu">RdYlBu</option> + <option value="Accent">Accent</option> + <option value="Spectral">Spectral</option> + <option value="Set1">Set1</option> + <option value="Set2">Set2</option> + <option value="Set3">Set3</option> + <option value="Dark2">Dark2</option> + <option value="Reds">Reds</option> + <option value="Oranges">Oranges</option> + <option value="Greens">Greens</option> + <option value="Blues">Blues</option> + <option value="Greys">Greys</option> + <option value="Purples">Purples</option> + <option value="Paired">Paired</option> + <option value="Pastel1">Pastel1</option> + <option value="Pastel2">Pastel2</option> + <option value="spring">spring</option> + <option value="summer">summer</option> + <option value="autumn">autumn</option> + <option value="winter">winter</option> + <option value="hot">hot</option> + <option value="coolwarm">coolwarm</option> + <option value="cool">cool</option> + <option value="seismic">seismic</option> + <option value="terrain">terrain</option> + <option value="ocean">ocean</option> + <option value="rainbow">rainbow</option> + <option value="bone">bone</option> + <option value="flag">flag</option> + <option value="prism">prism</option> + <option value="cubehelix">cubehelix</option> + <option value="binary">binary</option> + <option value="pink">pink</option> + <option value="gray">gray</option> + <option value="copper">copper</option> + <option value="BrBG">BrBG</option> + <option value="BuGn">BuGn</option> + <option value="BuPu">BuPu</option> + <option value="GnBu">GnBu</option> + <option value="OrRd">OrRd</option> + <option value="PiYG">PiYG</option> + <option value="PRGn">PRGn</option> + <option value="PuOr">PuOr</option> + <option value="PuRd">PuRd</option> + <option value="PuBu">PuBu</option> + <option value="RdBu">RdBu</option> + <option value="RdGy">RdGy</option> + <option value="RdPu">RdPu</option> + <option value="YlGn">YlGn</option> + <option value="PuBuGn">PuBuGn</option> + <option value="RdYlGn">RdYlGn</option> + <option value="YlGnBu">YlGnBu</option> + <option value="YlOrBr">YlOrBr</option> + <option value="YlOrRd">YlOrRd</option> + <option value="gist_gray">gist_gray</option> + <option value="gist_stern">gist_stern</option> + <option value="gist_earth">gist_earth</option> + <option value="gist_yarg">gist_yarg</option> + <option value="gist_ncar">gist_ncar</option> + <option value="gist_rainbow">gist_rainbow</option> + <option value="gist_heat">gist_heat</option> + <option value="gnuplot">gnuplot</option> + <option value="gnuplot2">gnuplot2</option> + <option value="CMRmap">CMRmap</option> + <option value="bwr">bwr</option> + <option value="hsv">hsv</option> + <option value="brg">brg</option> + <option value="jet">jet</option> + <option value="afmhot">afmhot</option> + <option value="Accent_r">Accent reversed</option> + <option value="Spectral_r">Spectral reversed</option> + <option value="Set1_r">Set1 reversed</option> + <option value="Set2_r">Set2 reversed</option> + <option value="Set3_r">Set3 reversed</option> + <option value="Dark2_r">Dark2 reversed</option> + <option value="Reds_r">Reds reversed</option> + <option value="Oranges_r">Oranges reversed</option> + <option value="Greens_r">Greens reversed</option> + <option value="Blues_r">Blues reversed</option> + <option value="Greys_r">Greys reversed</option> + <option value="Purples_r">Purples reversed</option> + <option value="Paired_r">Paired reversed</option> + <option value="Pastel1_r">Pastel1 reversed</option> + <option value="Pastel2_r">Pastel2 reversed</option> + <option value="spring_r">spring reversed</option> + <option value="summer_r">summer reversed</option> + <option value="autumn_r">autumn reversed</option> + <option value="winter_r">winter reversed</option> + <option value="hot_r">hot reversed</option> + <option value="coolwarm_r">coolwarm reversed</option> + <option value="cool_r">cool reversed</option> + <option value="seismic_r">seismic reversed</option> + <option value="terrain_r">terrain reversed</option> + <option value="ocean_r">ocean reversed</option> + <option value="rainbow_r">rainbow reversed</option> + <option value="bone_r">bone reversed</option> + <option value="flag_r">flag reversed</option> + <option value="prism_r">prism reversed</option> + <option value="cubehelix_r">cubehelix reversed</option> + <option value="binary_r">binary reversed</option> + <option value="pink_r">pink reversed</option> + <option value="gray_r">gray reversed</option> + <option value="copper_r">copper reversed</option> + <option value="BrBG_r">BrBG reversed</option> + <option value="BuGn_r">BuGn reversed</option> + <option value="BuPu_r">BuPu reversed</option> + <option value="GnBu_r">GnBu reversed</option> + <option value="OrRd_r">OrRd reversed</option> + <option value="PiYG_r">PiYG reversed</option> + <option value="PRGn_r">PRGn reversed</option> + <option value="PuOr_r">PuOr reversed</option> + <option value="PuRd_r">PuRd reversed</option> + <option value="PuBu_r">PuBu reversed</option> + <option value="RdBu_r">RdBu reversed</option> + <option value="RdGy_r">RdGy reversed</option> + <option value="RdPu_r">RdPu reversed</option> + <option value="YlGn_r">YlGn reversed</option> + <option value="PuBuGn_r">PuBuGn reversed</option> + <option value="RdYlBu_r" selected="True">RdYlBu reversed</option> + <option value="RdYlGn_r">RdYlGn reversed</option> + <option value="YlGnBu_r">YlGnBu reversed</option> + <option value="YlOrBr_r">YlOrBr reversed</option> + <option value="YlOrRd_r">YlOrRd reversed</option> + <option value="gist_gray_r">gist_gray reversed</option> + <option value="gist_stern_r">gist_stern reversed</option> + <option value="gist_earth_r">gist_earth reversed</option> + <option value="gist_yarg_r">gist_yarg reversed</option> + <option value="gist_ncar_r">gist_ncar reversed</option> + <option value="gist_rainbow_r">gist_rainbow reversed</option> + <option value="gist_heat_r">gist_heat reversed</option> + <option value="gnuplot_r">gnuplot reversed</option> + <option value="gnuplot2_r">gnuplot2 reversed</option> + <option value="CMRmap_r">CMRmap reversed</option> + <option value="bwr_r">bwr reversed</option> + <option value="hsv_r">hsv reversed</option> + <option value="brg_r">brg reversed</option> + <option value="jet_r">jet reversed</option> + <option value="afmhot_r">afmhot reversed</option> + </param> + </when> + </conditional> + <param name="border_color" type="color" value="#000000" label="Border color" optional="True" /> + </xml> + <xml name="color_coverage_macro"> + <param name="color" type="color" value="#000000" label="Color of track" optional="True" /> + <param name="alpha" type="float" value="1" min="0" max="1" label="level of transparency (alpha)" help="1 is opaque and 0 is totally transparent"/> + <conditional name="color_negative"> + <param name="color_negative_select" type="select" label="Use a different color for negative values"> + <option value="no" selected="True">No</option> + <option value="yes">Yes</option> + </param> + <when value="no" /> + <when value="yes"> + <param name="color" type="color" value="#000000" label="Color of negative values" optional="True" /> + </when> + </conditional> + </xml> + <xml name="overlay_macro"> + <param name="overlay_select" type="select" label="Overlay this track with the previous one:"> + <option value="no" selected="True">No</option> + <option value="yes">Yes</option> + <option value="share-y">Yes and keep same y axis</option> + </param> + </xml> + <xml name="type_coverage_macro"> + <conditional name="type_conditional"> + <param name="type_selector" type="select" label="Choose style of the plot."> + <option value="fill_option">fill</option> + <option value="line_option">line</option> + <option value="point_option">point</option> + </param> + <when value="line_option"> + <param name="width_line" type="float" value="0.5" optional="True" label="Width"/> + </when> + <when value="point_option"> + <param name="width_point" type="float" value="0.5" optional="True" label="Width"/> + </when> + <when value="fill_option" /> + </conditional> + </xml> + <xml name="minmax_macro"> + <param name="min_value" type="float" value="" optional="True" label="Minimum value"/> + <param name="max_value" type="float" value="" optional="True" label="Maximum value"/> + </xml> + <xml name="reading_bw_macro"> + <section name="reading_bw_conditional" title="Configure bigwig parameters" expanded="False"> + <param name="summary" type="select" label="Summary method"> + <option value="mean" selected="True">mean=mean value</option> + <option value="min">min=minimum value</option> + <option value="max">max=maximum value</option> + <option value="coverage">coverage=number of covered bases</option> + <option value="std">std=standard deviation</option> + </param> + <param name="number_of_bins" type="integer" value="" optional="True" label="Number of bins" /> + <param name="nans_to_zeros" type="boolean" truevalue="True" falsevalue="False" checked="false" + label="NAN's to zeros" /> + </section> + </xml> </macros>