Mercurial > repos > iuc > pygenometracks

comparison pyGenomeTracks.xml @ 9:2824d77cd8f8 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
author iuc
date Wed, 18 Nov 2020 21:33:46 +0000
parents 4ac4e7083b7e
children a1abfa420d9d
comparison
equal deleted inserted replaced
8:4ac4e7083b7e 9:2824d77cd8f8
19 19
20 20
21 sed '/^$/d' '$tracks_config' && 21 sed '/^$/d' '$tracks_config' &&
22 @BINARY@ 22 @BINARY@
23 --tracks '$tracks_config' 23 --tracks '$tracks_config'
24 #if $region and $region is not None: 24 --region '$region'
25 --region '$region' 25 #if $global_args.title != '':
26 --title '$global_args.title'
26 #end if 27 #end if
27 #if $global_args.title is not None: 28 #if $global_args.plotWidth != '':
28 --title '$global_args.title' 29 --plotWidth $global_args.plotWidth
30 #else:
31 --width $global_args.width
32 #end if
33 #if $global_args.height != '':
34 --height '$global_args.height'
29 #end if 35 #end if
30 --fontSize $global_args.fontsize 36 --fontSize $global_args.fontsize
31 --dpi $global_args.dpi 37 --dpi $global_args.dpi
32 --trackLabelFraction $global_args.trackLabelFraction 38 --trackLabelFraction $global_args.trackLabelFraction
33 --trackLabelHAlign $global_args.trackLabelHAlign 39 --trackLabelHAlign $global_args.trackLabelHAlign
555 #if $track.track_file_style_conditional.color != "": 561 #if $track.track_file_style_conditional.color != "":
556 color = $track.track_file_style_conditional.color 562 color = $track.track_file_style_conditional.color
557 #end if 563 #end if
558 alpha = $track.track_file_style_conditional.alpha 564 alpha = $track.track_file_style_conditional.alpha
559 line_width = $track.track_file_style_conditional.line_width 565 line_width = $track.track_file_style_conditional.line_width
560 #if $track.track_file_style_conditional.x_center != "": 566 #if $track.track_file_style_conditional.scalebar_pos.x_center != "":
561 x_center = $track.track_file_style_conditional.x_center 567 x_center = $track.track_file_style_conditional.scalebar_pos.x_center
562 #end if 568 #end if
563 #if $track.track_file_style_conditional.size != "": 569 #if $track.track_file_style_conditional.scalebar_pos.size != "":
564 size = $track.track_file_style_conditional.size 570 size = $track.track_file_style_conditional.scalebar_pos.size
571 #end if
572 #if $track.track_file_style_conditional.scalebar_pos.scalebar_start_position != "":
573 scalebar_start_position = $track.track_file_style_conditional.scalebar_pos.scalebar_start_position
574 #end if
575 #if $track.track_file_style_conditional.scalebar_pos.scalebar_end_position != "":
576 scalebar_end_position = $track.track_file_style_conditional.scalebar_pos.scalebar_end_position
565 #end if 577 #end if
566 where = $track.track_file_style_conditional.sb_where 578 where = $track.track_file_style_conditional.sb_where
567 #if $track.track_file_style_conditional.fontsize != "": 579 #if $track.track_file_style_conditional.fontsize != "":
568 fontsize = $track.track_file_style_conditional.fontsize 580 fontsize = $track.track_file_style_conditional.fontsize
569 #end if 581 #end if
578 </configfile> 590 </configfile>
579 </configfiles> 591 </configfiles>
580 <inputs> 592 <inputs>
581 <!--Arguments for pgt--> 593 <!--Arguments for pgt-->
582 <param argument="--region" type="text" label="Region of the genome to limit the operation" optional="false" 594 <param argument="--region" type="text" label="Region of the genome to limit the operation" optional="false"
583 help="The format is chr:start-end. Also valid is just to specify a chromosome, for example chr10:10-500" /> 595 help="The format is chr:start-end, for example chr10:10-500">
596 <validator type="expression" message="Region should be like chr10:10-500">'^[a-zA-Z0-9_]:\d+-\d+$'</validator>
597 </param>
584 <section name="global_args" title="Configure figure parameters" expanded="False"> 598 <section name="global_args" title="Configure figure parameters" expanded="False">
585 <param argument="--title" type="text" label="Plot title" help="If set, you may need to start by a spacer track"/> 599 <param argument="--title" type="text" label="Plot title" help="If set, you may need to start by a spacer track"/>
586 <param argument="--fontsize" type="integer" label="Font size for the labels of the plot" value="12"/> 600 <param argument="--fontsize" type="integer" label="Font size for the labels of the plot" value="12"/>
587 <param argument="--dpi" type="integer" label="Resolution (dpi)" value="72" 601 <param argument="--dpi" type="integer" label="Resolution (dpi)" value="72"
588 help="Resolution for the image in case the ouput is a raster graphics image (e.g png, jpg)"/> 602 help="Resolution for the image in case the ouput is a raster graphics image (e.g png, jpg)"/>
603 <param argument="--width" type="float" label="Figure width in cm" value="40"/>
604 <param argument="--plotWidth" type="float" label="Width in centimeters of the plotting (central) part" optional="true"
605 help="This will overwrite what has been defined as a figure width."/>
606 <param argument="--height" type="float" label="Figure height in centimeters" optional="true"
607 help="If not given, the figure height is computed based on the heights of the tracks. If given, the track height are proportionally scaled to match the desired figure height."/>
589 <param argument="--trackLabelFraction" type="float" label="Proportion of space dedicated to track labels" value="0.05" 608 <param argument="--trackLabelFraction" type="float" label="Proportion of space dedicated to track labels" value="0.05"
590 min="0" max="1"/> 609 min="0" max="1"/>
591 <param argument="--trackLabelHAlign" type="select" label="Horizontal alignment of track labels"> 610 <param argument="--trackLabelHAlign" type="select" label="Horizontal alignment of track labels">
592 <option value="left" selected="True">left</option> 611 <option value="left" selected="True">left</option>
593 <option value="right">right</option> 612 <option value="right">right</option>
962 <when value="scale_bar_option"> 981 <when value="scale_bar_option">
963 <expand macro="plot_title" /> 982 <expand macro="plot_title" />
964 <param name="color" type="color" label="Color of the scale bar" optional="True" /> 983 <param name="color" type="color" label="Color of the scale bar" optional="True" />
965 <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"/> 984 <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"/>
966 <param name="line_width" type="float" value="0.5" label="width of lines"/> 985 <param name="line_width" type="float" value="0.5" label="width of lines"/>
967 <param name="x_center" type="integer" label="coordinate where the scale bar should be plotted (center)" optional="True" 986 <section name="scalebar_pos" title="Set the scalebar position" expanded="true" help="You can optionally define one or multiple parameters below.">
968 help="If not set it will be in the middle of the plotted area."/> 987 <param name="scalebar_start_position" type="integer" label="coordinate where the scale bar should begin." optional="True"/>
969 <param name="size" type="integer" label="size of the scale bar" optional="True" 988 <param name="scalebar_end_position" type="integer" label="coordinate where the scale bar should end." optional="True"/>
970 help="If not set it will be the higher number that begins with 1, 2 or 5 followed by 0s that is less than half the plotted area."/> 989 <param name="x_center" type="integer" label="coordinate where the scale bar should be plotted (center)" optional="True"
990 help="If not set and cannot be deduced from others it will be in the middle of the plotted area."/>
991 <param name="size" type="integer" label="size of the scale bar" optional="True"
992 help="If not set and cannot be deduced from others it will be the higher number that begins with 1, 2 or 5 followed by 0s that is less than half the plotted area."/>
993 </section>
971 <param name="sb_where" type="select" label="where the size of the scale bar should appear relative to the bar"> 994 <param name="sb_where" type="select" label="where the size of the scale bar should appear relative to the bar">
972 <option value="left" selected="True">left</option> 995 <option value="left" selected="True">left</option>
973 <option value="right">right</option> 996 <option value="right">right</option>
974 <option value="bottom">below</option> 997 <option value="bottom">below</option>
975 <option value="top">above</option> 998 <option value="top">above</option>
1172 <param name="track_file_style_selector" value="vlines_track_option" /> 1195 <param name="track_file_style_selector" value="vlines_track_option" />
1173 <param name="track_input_bed_single" value="domains.bed" ftype="bed" /> 1196 <param name="track_input_bed_single" value="domains.bed" ftype="bed" />
1174 </conditional> 1197 </conditional>
1175 </repeat> 1198 </repeat>
1176 <param name="image_file_format" value="png" /> 1199 <param name="image_file_format" value="png" />
1177 <output name="outFileName" file="master_TADs_plot.png" ftype="png" compare="sim_size" delta="35000" /> 1200 <output name="outFileName" file="master_TADs_plot.png" ftype="png" compare="sim_size" delta="100" />
1178 </test> 1201 </test>
1179 <!--test 2--> 1202 <!--test 2-->
1180 <test> 1203 <test>
1181 <param name="region" value="chrX:3000000-3500000"/> 1204 <param name="region" value="chrX:3000000-3500000"/>
1182 <repeat name="tracks"> 1205 <repeat name="tracks">
1236 <param name="show_data" value="true" /> 1259 <param name="show_data" value="true" />
1237 <param name="invert_orientation" value="true" /> 1260 <param name="invert_orientation" value="true" />
1238 </conditional> 1261 </conditional>
1239 </repeat> 1262 </repeat>
1240 <param name="image_file_format" value="png" /> 1263 <param name="image_file_format" value="png" />
1241 <output name="outFileName" file="bigwig_multiple.png" ftype="png" compare="sim_size" delta="35000" /> 1264 <output name="outFileName" file="bigwig_multiple.png" ftype="png" compare="sim_size" delta="100" />
1242 </test> 1265 </test>
1243 <!--test 3--> 1266 <!--test 3-->
1244 <test> 1267 <test>
1245 <param name="region" value="chrX:3000000-3500000"/> 1268 <param name="region" value="chrX:3000000-3500000"/>
1246 <repeat name="tracks"> 1269 <repeat name="tracks">
1467 </conditional> 1490 </conditional>
1468 <param name="display" value="interleaved" /> 1491 <param name="display" value="interleaved" />
1469 </conditional> 1492 </conditional>
1470 </repeat> 1493 </repeat>
1471 <param name="image_file_format" value="png" /> 1494 <param name="image_file_format" value="png" />
1472 <output name="outFileName" file="master_TADs_BW_plot.png" ftype="png" compare="sim_size" delta="35000" /> 1495 <output name="outFileName" file="master_TADs_BW_plot.png" ftype="png" compare="sim_size" delta="100" />
1473 </test> 1496 </test>
1474 <!--test 4--> 1497 <!--test 4-->
1475 <test> 1498 <test>
1476 <param name="region" value="X:2700000-3100000"/> 1499 <param name="region" value="X:2700000-3100000"/>
1477 <repeat name="tracks"> 1500 <repeat name="tracks">
1505 <param name="track_file_style_selector" value="xaxis_option" /> 1528 <param name="track_file_style_selector" value="xaxis_option" />
1506 <param name="xaxis_where" value="bottom" /> 1529 <param name="xaxis_where" value="bottom" />
1507 </conditional> 1530 </conditional>
1508 </repeat> 1531 </repeat>
1509 <param name="image_file_format" value="png" /> 1532 <param name="image_file_format" value="png" />
1510 <output name="outFileName" file="test_alpha.png" ftype="png" compare="sim_size" delta="35000" /> 1533 <output name="outFileName" file="test_alpha.png" ftype="png" compare="sim_size" delta="100" />
1511 </test> 1534 </test>
1512 <!--test 5--> 1535 <!--test 5-->
1513 <test> 1536 <test>
1514 <param name="region" value="X:3000000-3300000"/> 1537 <param name="region" value="X:3000000-3300000"/>
1515 <repeat name="tracks"> 1538 <repeat name="tracks">
1543 </conditional> 1566 </conditional>
1544 <param name="spacer_height" value="1"/> 1567 <param name="spacer_height" value="1"/>
1545 </conditional> 1568 </conditional>
1546 </repeat> 1569 </repeat>
1547 <param name="image_file_format" value="png" /> 1570 <param name="image_file_format" value="png" />
1548 <output name="outFileName" file="test_gtf_bed4.png" ftype="png" compare="sim_size" delta="35000" /> 1571 <output name="outFileName" file="test_gtf_bed4.png" ftype="png" compare="sim_size" delta="100" />
1549 </test> 1572 </test>
1550 <!--test 6--> 1573 <!--test 6-->
1551 <test> 1574 <test>
1552 <param name="region" value="X:2760000-2802000"/> 1575 <param name="region" value="X:2760000-2802000"/>
1553 <repeat name="tracks"> 1576 <repeat name="tracks">
1617 <param name="track_file_style_selector" value="xaxis_option" /> 1640 <param name="track_file_style_selector" value="xaxis_option" />
1618 <param name="xaxis_where" value="bottom" /> 1641 <param name="xaxis_where" value="bottom" />
1619 </conditional> 1642 </conditional>
1620 </repeat> 1643 </repeat>
1621 <param name="image_file_format" value="png" /> 1644 <param name="image_file_format" value="png" />
1622 <output name="outFileName" file="test_narrowPeak.png" ftype="png" compare="sim_size" delta="35000" /> 1645 <output name="outFileName" file="test_narrowPeak.png" ftype="png" compare="sim_size" delta="100" />
1623 </test> 1646 </test>
1624 <!--test 7--> 1647 <!--test 7-->
1625 <test> 1648 <test>
1626 <param name="region" value="chrX:3300000-3500000"/> 1649 <param name="region" value="chrX:3300000-3500000"/>
1627 <repeat name="tracks"> 1650 <repeat name="tracks">
1722 <param name="all_labels_inside" value="true" /> 1745 <param name="all_labels_inside" value="true" />
1723 </conditional> 1746 </conditional>
1724 </conditional> 1747 </conditional>
1725 </repeat> 1748 </repeat>
1726 <param name="image_file_format" value="png" /> 1749 <param name="image_file_format" value="png" />
1727 <output name="outFileName" file="test_gtf_flybase_param.png" ftype="png" compare="sim_size" delta="35000" /> 1750 <output name="outFileName" file="test_gtf_flybase_param.png" ftype="png" compare="sim_size" delta="100" />
1728 </test> 1751 </test>
1729 <!--test 8--> 1752 <!--test 8-->
1730 <test> 1753 <test>
1731 <param name="region" value="chrX:3300000-3500000"/> 1754 <param name="region" value="chrX:3300000-3500000"/>
1732 <repeat name="tracks"> 1755 <repeat name="tracks">
1764 </section> 1787 </section>
1765 </conditional> 1788 </conditional>
1766 </conditional> 1789 </conditional>
1767 </repeat> 1790 </repeat>
1768 <param name="image_file_format" value="png" /> 1791 <param name="image_file_format" value="png" />
1769 <output name="outFileName" file="test_ucsc_param.png" ftype="png" compare="sim_size" delta="35000" /> 1792 <output name="outFileName" file="test_ucsc_param.png" ftype="png" compare="sim_size" delta="100" />
1770 </test> 1793 </test>
1771 <!--test 9--> 1794 <!--test 9-->
1772 <test> 1795 <test>
1773 <param name="region" value="X:3133000-3138000"/> 1796 <param name="region" value="X:3133000-3138000"/>
1774 <repeat name="tracks"> 1797 <repeat name="tracks">
1823 <param name="track_file_style_selector" value="vlines_track_option" /> 1846 <param name="track_file_style_selector" value="vlines_track_option" />
1824 <param name="track_input_bed_single" value="dm3_subset_BDGP5.78_asbed4.bed.gz" ftype="bed" /> 1847 <param name="track_input_bed_single" value="dm3_subset_BDGP5.78_asbed4.bed.gz" ftype="bed" />
1825 </conditional> 1848 </conditional>
1826 </repeat> 1849 </repeat>
1827 <param name="image_file_format" value="png" /> 1850 <param name="image_file_format" value="png" />
1828 <output name="outFileName" file="test_arrowhead_zoom.png" ftype="png" compare="sim_size" delta="35000" /> 1851 <output name="outFileName" file="test_arrowhead_zoom.png" ftype="png" compare="sim_size" delta="100" />
1829 </test> 1852 </test>
1830 <!--test 10--> 1853 <!--test 10-->
1831 <test> 1854 <test>
1832 <param name="region" value="X:3340000-3380000"/> 1855 <param name="region" value="X:3340000-3380000"/>
1833 <repeat name="tracks"> 1856 <repeat name="tracks">
1873 <param name="type_selector" value="line_option" /> 1896 <param name="type_selector" value="line_option" />
1874 </conditional> 1897 </conditional>
1875 </conditional> 1898 </conditional>
1876 </repeat> 1899 </repeat>
1877 <param name="image_file_format" value="png" /> 1900 <param name="image_file_format" value="png" />
1878 <output name="outFileName" file="test_middle_triangle.png" ftype="png" compare="sim_size" delta="35000" /> 1901 <output name="outFileName" file="test_middle_triangle.png" ftype="png" compare="sim_size" delta="100" />
1879 </test> 1902 </test>
1880 <!--test 11--> 1903 <!--test 11-->
1881 <test> 1904 <test>
1882 <param name="region" value="chrX:3250000-3400000"/> 1905 <param name="region" value="chrX:3250000-3400000"/>
1883 <repeat name="tracks"> 1906 <repeat name="tracks">
1930 <param name="plot_horizontal_lines" value="false" /> 1953 <param name="plot_horizontal_lines" value="false" />
1931 </conditional> 1954 </conditional>
1932 </conditional> 1955 </conditional>
1933 </repeat> 1956 </repeat>
1934 <param name="image_file_format" value="png" /> 1957 <param name="image_file_format" value="png" />
1935 <output name="outFileName" file="test_TADs_bdgm.png" ftype="png" compare="sim_size" delta="35000" /> 1958 <output name="outFileName" file="test_TADs_bdgm.png" ftype="png" compare="sim_size" delta="100" />
1936 </test> 1959 </test>
1937 <!--test 12--> 1960 <!--test 12-->
1938 <test> 1961 <test>
1939 <param name="region" value="chrX:3000000-3300000"/> 1962 <param name="region" value="chrX:3000000-3300000"/>
1940 <repeat name="tracks"> 1963 <repeat name="tracks">
1980 <param name="max_value" value="5"/> 2003 <param name="max_value" value="5"/>
1981 <param name="invert_orientation" value="true" /> 2004 <param name="invert_orientation" value="true" />
1982 </conditional> 2005 </conditional>
1983 </repeat> 2006 </repeat>
1984 <param name="image_file_format" value="png" /> 2007 <param name="image_file_format" value="png" />
1985 <output name="outFileName" file="test_link.png" ftype="png" compare="sim_size" delta="35000" /> 2008 <output name="outFileName" file="test_link.png" ftype="png" compare="sim_size" delta="100" />
1986 </test> 2009 </test>
1987 <!--test 13--> 2010 <!--test 13-->
1988 <test> 2011 <test>
1989 <param name="region" value="chrX:3000000-3300000"/> 2012 <param name="region" value="chrX:3000000-3300000"/>
1990 <repeat name="tracks"> 2013 <repeat name="tracks">
2033 </conditional> 2056 </conditional>
2034 <param name="compact_arcs_level" value="2" /> 2057 <param name="compact_arcs_level" value="2" />
2035 </conditional> 2058 </conditional>
2036 </repeat> 2059 </repeat>
2037 <param name="image_file_format" value="png" /> 2060 <param name="image_file_format" value="png" />
2038 <output name="outFileName" file="test_link2.png" ftype="png" compare="sim_size" delta="35000" /> 2061 <output name="outFileName" file="test_link2.png" ftype="png" compare="sim_size" delta="100" />
2039 </test> 2062 </test>
2040 <!--test 14--> 2063 <!--test 14-->
2041 <test> 2064 <test>
2042 <param name="region" value="chrX:3000000-3300000"/> 2065 <param name="region" value="chrX:3000000-3300000"/>
2043 <section name="global_args"> 2066 <section name="global_args">
2063 <param name="track_file_style_selector" value="scale_bar_option" /> 2086 <param name="track_file_style_selector" value="scale_bar_option" />
2064 <param name="title" value="scalebar where = right x_center = 3200000 size = 100002 fontsize = 8 line_width =2 color = red alpha = 0.5" /> 2087 <param name="title" value="scalebar where = right x_center = 3200000 size = 100002 fontsize = 8 line_width =2 color = red alpha = 0.5" />
2065 <param name="color" value="red"/> 2088 <param name="color" value="red"/>
2066 <param name="alpha" value="0.5"/> 2089 <param name="alpha" value="0.5"/>
2067 <param name="line_width" value="2"/> 2090 <param name="line_width" value="2"/>
2068 <param name="x_center" value="3200000"/> 2091 <section name="scalebar_pos">
2069 <param name="size" value="100002"/> 2092 <param name="x_center" value="3200000"/>
2093 <param name="size" value="100002"/>
2094 </section>
2070 <param name="sb_where" value="right"/> 2095 <param name="sb_where" value="right"/>
2071 <param name="fontsize" value="8"/> 2096 <param name="fontsize" value="8"/>
2072 <param name="spacer_height" value="4"/> 2097 <param name="spacer_height" value="4"/>
2073 </conditional> 2098 </conditional>
2074 </repeat> 2099 </repeat>
2075 <param name="image_file_format" value="png" /> 2100 <param name="image_file_format" value="png" />
2076 <output name="outFileName" file="test_scale_bar.png" ftype="png" compare="sim_size" delta="35000" /> 2101 <output name="outFileName" file="test_scale_bar.png" ftype="png" compare="sim_size" delta="100" />
2077 </test> 2102 </test>
2078 <!--test 15--> 2103 <!--test 15-->
2079 <test> 2104 <test>
2080 <param name="region" value="chrX:3300000-3500000"/> 2105 <param name="region" value="chrX:3300000-3500000"/>
2081 <repeat name="tracks"> 2106 <repeat name="tracks">
2130 </section> 2155 </section>
2131 </conditional> 2156 </conditional>
2132 </conditional> 2157 </conditional>
2133 </repeat> 2158 </repeat>
2134 <param name="image_file_format" value="png" /> 2159 <param name="image_file_format" value="png" />
2135 <output name="outFileName" file="test_tssarrow.png" ftype="png" compare="sim_size" delta="35000" /> 2160 <output name="outFileName" file="test_tssarrow.png" ftype="png" compare="sim_size" delta="100" />
2136 </test> 2161 </test>
2137 <!--test 16--> 2162 <!--test 16-->
2138 <test> 2163 <test>
2139 <param name="region" value="X:2700000-3100000"/> 2164 <param name="region" value="X:2700000-3100000"/>
2140 <section name="global_args"> 2165 <section name="global_args">
2171 <param name="track_file_style_selector" value="xaxis_option" /> 2196 <param name="track_file_style_selector" value="xaxis_option" />
2172 <param name="xaxis_where" value="bottom" /> 2197 <param name="xaxis_where" value="bottom" />
2173 </conditional> 2198 </conditional>
2174 </repeat> 2199 </repeat>
2175 <param name="image_file_format" value="png" /> 2200 <param name="image_file_format" value="png" />
2176 <output name="outFileName" file="test_alpha_dec.png" ftype="png" compare="sim_size" delta="35000" /> 2201 <output name="outFileName" file="test_alpha_dec.png" ftype="png" compare="sim_size" delta="1000" />
2177 </test> 2202 </test>
2178 <!--test 17--> 2203 <!--test 17-->
2179 <test> 2204 <test>
2180 <param name="region" value="chr2:73,800,000-75,744,000"/> 2205 <param name="region" value="chr2:73,800,000-75,744,000"/>
2181 <repeat name="tracks"> 2206 <repeat name="tracks">
2294 <param name="track_file_style_selector" value="xaxis_option" /> 2319 <param name="track_file_style_selector" value="xaxis_option" />
2295 <param name="xaxis_where" value="bottom" /> 2320 <param name="xaxis_where" value="bottom" />
2296 </conditional> 2321 </conditional>
2297 </repeat> 2322 </repeat>
2298 <param name="image_file_format" value="png" /> 2323 <param name="image_file_format" value="png" />
2299 <output name="outFileName" file="test_log.png" ftype="png" compare="sim_size" delta="35000" /> 2324 <output name="outFileName" file="test_log.png" ftype="png" compare="sim_size" delta="100" />
2300 </test> 2325 </test>
2301 <!--test 18--> 2326 <!--test 18-->
2302 <test> 2327 <test>
2303 <param name="region" value="chrX:2700000-3100000"/> 2328 <param name="region" value="chrX:2700000-3100000"/>
2304 <repeat name="tracks"> 2329 <repeat name="tracks">
2372 <param name="min_value" value="-30" /> 2397 <param name="min_value" value="-30" />
2373 <param name="max_value" value="30" /> 2398 <param name="max_value" value="30" />
2374 </conditional> 2399 </conditional>
2375 </repeat> 2400 </repeat>
2376 <param name="image_file_format" value="png" /> 2401 <param name="image_file_format" value="png" />
2377 <output name="outFileName" file="test_operation.png" ftype="png" compare="sim_size" delta="35000" /> 2402 <output name="outFileName" file="test_operation.png" ftype="png" compare="sim_size" delta="100" />
2378 </test> 2403 </test>
2379 <!--test 19--> 2404 <!--test 19-->
2380 <test> 2405 <test>
2381 <param name="region" value="chr2:73,800,000-75,744,000"/> 2406 <param name="region" value="chr2:73,800,000-75,744,000"/>
2382 <repeat name="tracks"> 2407 <repeat name="tracks">
2503 <param name="track_file_style_selector" value="xaxis_option" /> 2528 <param name="track_file_style_selector" value="xaxis_option" />
2504 <param name="xaxis_where" value="bottom" /> 2529 <param name="xaxis_where" value="bottom" />
2505 </conditional> 2530 </conditional>
2506 </repeat> 2531 </repeat>
2507 <param name="image_file_format" value="png" /> 2532 <param name="image_file_format" value="png" />
2508 <output name="outFileName" file="test_log_grid.png" ftype="png" compare="sim_size" delta="35000" /> 2533 <output name="outFileName" file="test_log_grid.png" ftype="png" compare="sim_size" delta="100" />
2509 </test> 2534 </test>
2510 <!--test 20--> 2535 <!--test 20-->
2511 <test> 2536 <test>
2512 <param name="region" value="chrX:3000000-3300000"/> 2537 <param name="region" value="chrX:3000000-3300000"/>
2513 <repeat name="tracks"> 2538 <repeat name="tracks">
2553 <param name="color" value="RdYlGn" /> 2578 <param name="color" value="RdYlGn" />
2554 </conditional> 2579 </conditional>
2555 <param name="line_width" value="3" /> 2580 <param name="line_width" value="3" />
2556 <param name="invert_orientation" value="true" /> 2581 <param name="invert_orientation" value="true" />
2557 <param name="title" value="links line_width = 3 color RdYlGn" /> 2582 <param name="title" value="links line_width = 3 color RdYlGn" />
2583 <param name="height" value="3" />
2558 </conditional> 2584 </conditional>
2559 </repeat> 2585 </repeat>
2560 <repeat name="tracks"> 2586 <repeat name="tracks">
2561 <conditional name="track_file_style_conditional"> 2587 <conditional name="track_file_style_conditional">
2562 <param name="track_file_style_selector" value="spacer_option" /> 2588 <param name="track_file_style_selector" value="spacer_option" />
2595 </conditional> 2621 </conditional>
2596 <param name="line_width" value="3" /> 2622 <param name="line_width" value="3" />
2597 <param name="invert_orientation" value="true" /> 2623 <param name="invert_orientation" value="true" />
2598 <param name="use_middle" value="true" /> 2624 <param name="use_middle" value="true" />
2599 <param name="title" value="links line_width = 3 color RdYlGn use_middle = true" /> 2625 <param name="title" value="links line_width = 3 color RdYlGn use_middle = true" />
2626 <param name="height" value="3" />
2600 </conditional> 2627 </conditional>
2601 </repeat> 2628 </repeat>
2602 <repeat name="tracks"> 2629 <repeat name="tracks">
2603 <conditional name="track_file_style_conditional"> 2630 <conditional name="track_file_style_conditional">
2604 <param name="track_file_style_selector" value="vlines_track_option" /> 2631 <param name="track_file_style_selector" value="vlines_track_option" />
2605 <param name="track_input_bed_single" value="tad_classification.bed" ftype="bed" /> 2632 <param name="track_input_bed_single" value="tad_classification.bed" ftype="bed" />
2606 <param name="line_width" value="3" /> 2633 <param name="line_width" value="3" />
2607 </conditional> 2634 </conditional>
2608 </repeat> 2635 </repeat>
2609 <param name="image_file_format" value="png" /> 2636 <param name="image_file_format" value="png" />
2610 <output name="outFileName" file="test_arcs_use_middle.png" ftype="png" compare="sim_size" delta="35000" /> 2637 <output name="outFileName" file="test_arcs_use_middle.png" ftype="png" compare="sim_size" delta="1200" />
2638 </test>
2639 <!--test 21-->
2640 <test>
2641 <param name="region" value="X:3000000-3600000"/>
2642 <section name="global_args">
2643 <param name="trackLabelFraction" value="0.3"/>
2644 <param name="plotWidth" value="12"/>
2645 <param name="dpi" value="20"/>
2646 </section>
2647 <repeat name="tracks">
2648 <conditional name="track_file_style_conditional">
2649 <param name="track_file_style_selector" value="scale_bar_option" />
2650 <param name="title" value="scalebar where = right" />
2651 <param name="where" value="right" />
2652 <param name="spacer_height" value="0.5"/>
2653 </conditional>
2654 </repeat>
2655 <repeat name="tracks">
2656 <conditional name="track_file_style_conditional">
2657 <param name="track_file_style_selector" value="scale_bar_option" />
2658 <param name="title" value="scalebar scalebar_start_position = 3200000" />
2659 <section name="scalebar_pos">
2660 <param name="scalebar_start_position" value="3200000"/>
2661 </section>
2662 <param name="spacer_height" value="0.5"/>
2663 </conditional>
2664 </repeat>
2665 <repeat name="tracks">
2666 <conditional name="track_file_style_conditional">
2667 <param name="track_file_style_selector" value="scale_bar_option" />
2668 <param name="title" value="scalebar scalebar_start_position = 3200000 scalebar_end_position = 3250000" />
2669 <section name="scalebar_pos">
2670 <param name="scalebar_start_position" value="3200000"/>
2671 <param name="scalebar_start_position" value="3250000"/>
2672 </section>
2673 <param name="spacer_height" value="0.5"/>
2674 </conditional>
2675 </repeat>
2676 <repeat name="tracks">
2677 <conditional name="track_file_style_conditional">
2678 <param name="track_file_style_selector" value="scale_bar_option" />
2679 <param name="title" value="scalebar scalebar_start_position = 3200000 x_center = 3250000" />
2680 <section name="scalebar_pos">
2681 <param name="scalebar_start_position" value="3200000"/>
2682 <param name="x_center" value="3250000"/>
2683 </section>
2684 <param name="spacer_height" value="0.5"/>
2685 </conditional>
2686 </repeat>
2687 <repeat name="tracks">
2688 <conditional name="track_file_style_conditional">
2689 <param name="track_file_style_selector" value="scale_bar_option" />
2690 <param name="title" value="scalebar scalebar_start_position = 3200000 size = 50000" />
2691 <section name="scalebar_pos">
2692 <param name="scalebar_start_position" value="3200000"/>
2693 <param name="size" value="50000"/>
2694 </section>
2695 <param name="spacer_height" value="0.5"/>
2696 </conditional>
2697 </repeat>
2698 <repeat name="tracks">
2699 <conditional name="track_file_style_conditional">
2700 <param name="track_file_style_selector" value="scale_bar_option" />
2701 <param name="title" value="scalebar scalebar_end_position = 3200000 size = 50000" />
2702 <section name="scalebar_pos">
2703 <param name="scalebar_end_position" value="3200000"/>
2704 <param name="size" value="50000"/>
2705 </section>
2706 <param name="spacer_height" value="0.5"/>
2707 </conditional>
2708 </repeat>
2709 <repeat name="tracks">
2710 <conditional name="track_file_style_conditional">
2711 <param name="track_file_style_selector" value="xaxis_option" />
2712 <param name="xaxis_where" value="bottom" />
2713 </conditional>
2714 </repeat>
2715 <param name="image_file_format" value="png" />
2716 <output name="outFileName" file="master_scale_bar_startend.png" ftype="png" compare="sim_size" delta="100" />
2611 </test> 2717 </test>
2612 </tests> 2718 </tests>
2613 <help><![CDATA[ 2719 <help><![CDATA[
2614 2720
2615 pyGenomeTracks 2721 pyGenomeTracks
2617 2723
2618 **pyGenomeTracks** is a visualization tool which aims to produce high-quality genome browser tracks that are highly customizable. 2724 **pyGenomeTracks** is a visualization tool which aims to produce high-quality genome browser tracks that are highly customizable.
2619 Currently, it is possible to plot: 2725 Currently, it is possible to plot:
2620 2726
2621 - bigwig 2727 - bigwig
2622 - bed (many options) 2728 - bed/gtf (many options)
2623 - bedgraph 2729 - bedgraph
2624 - links (represented as arcs) 2730 - epilogos
2625 - Hi-C matrices 2731 - narrow peaks
2732 - links
2733 - Hi-C matrices (cool or HiCExplorer h5)
2626 2734
2627 _________________ 2735 _________________
2628 2736
2629 Usage 2737 Usage
2630 ----- 2738 -----
2631 2739
2632 This tool takes various types of tracks as input: 2740 This tool takes various types of tracks as input:
2633 2741
2742 - **Hi-C tracks:**
2743 - **TAD vizualisation:** corrected Hi-C contact matrix to plot a contact heatmap. It is recommended to follow HiCExplorer's ``hicPlotMatrix`` instructions. Boundaries file can used, which is the output of HiCExplorer's ``hicFindTADs`` in bed format. If selected, TADs will be drawn directly on the contact heatmap.
2744 - **TAD score:** display TAD seperation score computed by HiCExplorer's ``hicFindTADs``.
2634 - **Chromatin states:** display blocks of different colors following a bed file. 2745 - **Chromatin states:** display blocks of different colors following a bed file.
2635 - **Gene track / Bed Track:** display genes or bed files. Labels like gene names can be toggled on or off. 2746 - **Gene track / Bed Track:** display genes or annotations in bed/gtf files. Labels like gene names can be toggled on or off.
2747 - **Link track:** display links (pair of coordinates) as arcs, triangles or loops.
2748 - **NarrowPeak track:** display narrowPeak (encode format) as boxes or as curve (reconstructed peak).
2636 - **Bigwig track:** generic bigwig track plotting. 2749 - **Bigwig track:** generic bigwig track plotting.
2637 - **Bedgraph track:** generic bedgraph track plotting. 2750 - **Bedgraph track:** generic bedgraph track plotting.
2638 - **Bedgraph matrix track** is used to specifically plot bm files computed by HiCExplorer's ``hicFindTADs`` (TAD seperation scores). 2751 - **Bedgraph matrix track** is used to specifically plot bm files computed by HiCExplorer's ``hicFindTADs`` (TAD seperation scores).
2639 - **Vlines:** vertical lines drawn on top of all tracks following a bed file. It is used as a visual support where regions start / end over all tracks, for example to display TAD boundaries computed by HiCExplorer's ``hicFindTADs``. 2752 - **Vlines:** vertical lines drawn on top of all tracks following a bed file. It is used as a visual support where regions start / end over all tracks, for example to display TAD boundaries computed by HiCExplorer's ``hicFindTADs``.
2753 - **Hlines:** horizontal lines drawn either by themselves or on top of other tracks.
2640 - **Spacer:** Add some space between two tracks. 2754 - **Spacer:** Add some space between two tracks.
2641 - **Hi-C tracks:** 2755 - **X-axis:** Plot x-axis scale wherever you want.
2642 - **TAD vizualisation:** corrected Hi-C contact matrix to plot a contact heatmap. It is recommended to follow HiCExplorer's ``hicPlotMatrix`` instructions. Boundaries file can used, which is the output of HiCExplorer's ``hicFindTADs`` in bed format. If selected, TADs will be drawn directly on the contact heatmap. 2756 - **Scale bar track:** Plot scale bar.
2643 - **TAD score:** display TAD seperation score computed by HiCExplorer's ``hicFindTADs``.
2644
2645 2757
2646 For each track, parameters for the color, the width or the font size can be defined. 2758 For each track, parameters for the color, the width or the font size can be defined.
2647 2759
2648 _________________ 2760 _________________
2649 2761
2650 Output 2762 Output
2651 ------ 2763 ------
2652 2764
2653 **pyGenomeTracks** output is similar to a genome browser screen-shot that besides the usual genes, and score data (like bigwig or bedgraph files) 2765 **pyGenomeTracks** output is similar to a genome browser screen-shot that besides the usual genes, and score data (like bigwig or bedgraph files)
2654 also contains Hi-C data. The plot is composed of tracks that need to be specified. 2766 may also contains Hi-C data. The plot is composed of tracks that need to be specified.
2655 Below is represented the 85 Mb to 110 Mb region from human chromosome 2 visualized using **pyGenomeTracks**. 2767 Below is represented the 85 Mb to 110 Mb region from human chromosome 2 visualized using **pyGenomeTracks**.
2656 TADs were computed by HiCExplorer's ``hicFindTADs``. The additional tracks added correspond to: 2768 TADs were computed by HiCExplorer's ``hicFindTADs``. The additional tracks added correspond to:
2657 TAD-separation score (as reported by HiCExplorer's ``hicFindTADs``), chromatin states, 2769 TAD-separation score (as reported by HiCExplorer's ``hicFindTADs``), chromatin states,
2658 principal component 1 (A/B compartment) computed using HiCExplorer's ``hicPCA``, ChIP-seq coverage for the H3K27ac mark, DNA methylation, and a gene track. 2770 principal component 1 (A/B compartment) computed using HiCExplorer's ``hicPCA``, ChIP-seq coverage for the H3K27ac mark, DNA methylation, and a gene track.
2659 Data are from mouse cardiac myocytes, published by `Nothjunge et al. (2017)`_. 2771 Data are from mouse cardiac myocytes, published by `Nothjunge et al. (2017)`_.
2661 .. image:: $PATH_TO_IMAGES/pyGenomeTracks.png 2773 .. image:: $PATH_TO_IMAGES/pyGenomeTracks.png
2662 :width: 70 % 2774 :width: 70 %
2663 2775
2664 _________________ 2776 _________________
2665 2777
2666 | For more information about pyGenomeTracks please consider our documentation on github_ 2778 | For more information about pyGenomeTracks please consider our documentation on readthedocs_ or github_
2667 2779
2780 .. _readthedocs: https://pygenometracks.readthedocs.io
2668 .. _github: https://github.com/deeptools/pyGenomeTracks 2781 .. _github: https://github.com/deeptools/pyGenomeTracks
2669 .. _`Nothjunge et al. (2017)`: https://www.nature.com/articles/s41467-017-01724-9 2782 .. _`Nothjunge et al. (2017)`: https://www.nature.com/articles/s41467-017-01724-9
2670 ]]></help> 2783 ]]></help>
2671 <expand macro="citations" /> 2784 <expand macro="citations" />
2672 </tool> 2785 </tool>