/tools/ceas/sitepro.xml
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1<tool name="SitePro: Aggregation plot tool for signal profiling" id="ceas_sitepro"> 2 <description>Draw the score profile near a given interval</description> 3 <command interpreter="command">/bin/bash $shscript</command> 4 <inputs> 5 <conditional name="mode"> 6 <param name="mode_select" type="select" label="Sitepro behaviour mode" force_select="true"> 7 <option value="single"> 1 wiggle / bigwig vs 1 BED file</option> 8 <option value="multiwig"> multiple wiggle / bigwig vs 1 BED</option> 9 <option value="multibed"> multiple BED vs 1 wiggle / bigwig</option> 10 </param> 11 12 <when value="single"> 13 <param ftype="wig" format="wig,bigwig" name="wfile" type="data" label="Wiggle / bigwig file"/> 14 <param ftype="bed" format="bed" name="bfile" type="data" label="BED file(100,000 lines max)"/> 15 </when> 16 17 <when value="multiwig"> 18 <param format="wig,bigwig" name="wfile" type="data" label="Wiggle / bigwig file"/> 19 <param name="label" type="text" label="Wiggle label" optional="false" /> 20 <repeat name="more" title="wiggle / bigwig file"> 21 <param format="wig,bigwig" name="wig" type="data" label="Select another wiggle / bigwig file"/> 22 <param name="label" type="text" label="Wiggle label" optional="false" /> 23 </repeat> 24 <param format="bed" name="bfile" type="data" 25 label="BED file"/> 26 </when> 27 28 <when value="multibed"> 29 <param format="bed" name="bfile" type="data" label="BED file(100,000 lines max)"/> 30 <param name="label" type="text" label="BED label" optional="false" /> 31 <repeat name="more" title="BED file"> 32 <param format="bed" name="bfile" type="data" label="Select another BED file(100,000 lines max)"/> 33 <param name="label" type="text" label="BED label" optional="false" /> 34 </repeat> 35 <param format="wig,bigwig" name="wfile" type="data" label="Wiggle / bigwig file"/> 36 </when> 37 38 </conditional> 39 40 <param name="span" type="integer" label="Span" value="1000"> 41 <validator type="in_range" max="1000000" min="100" message="Span is out of range, Span has to be between 100 to 1000000" /> 42 </param> 43 <param name="pfres" type="integer" label="Profiling Resolution" value="50"> 44 <validator type="in_range" max="1000" min="10" message="Profiling Resolution is out of range, Profiling Resolution has to be between 10 to 1000" /> 45 </param> 46 <param name="dir" type="boolean" label="consider the direction (+/-) while profiling" checked="no" truevalue="--dir" falsevalue=" " /> 47 </inputs> 48 <outputs> 49 <data format="pdf" name="output" /> 50 <data format="txt" name="log" label="sitepro job log" /> 51 <data format="txt" name="dump" label="txt file with profiles" /> 52 </outputs> 53 54 <configfiles> 55 <configfile name="shscript"> 56#!/bin/bash 57#import os 58 59#set $dollar = chr(36) 60#set $gt = chr(62) 61#set $lt = chr(60) 62#set $ad = chr(38) 63 64#set $path = $os.path.abspath($__app__.config.tool_path) 65 66##REMOVING WIG VALIDATORS 67##note: validator for wig file size 68##if [ $mode.wfile != "None" ];then 69## wfilesize=`du -b $mode.wfile | awk '{print ${dollar}1}'` 70## 71## if [[ ${dollar}wfilesize -gt 2097152000 ]];then 72## echo "wfile file is too big! 2GB is the maximum!" ${gt}${ad}2 73## exit; 74## fi 75##fi 76 77##note: validator for wig label 78#if $mode.mode_select == "multiwig" 79 wiglabel=`echo $mode.label |awk '{print length(${dollar}0)}'` 80 if [[ ${dollar}wiglabel -gt 255 ]];then 81 echo "Wig Label exceed the limit of 255 characters!" ${gt}${ad}2; 82 exit; 83 fi 84 if [[ ${dollar}wiglabel -eq 0 ]];then 85 echo "Wig Label is required!" ${gt}${ad}2; 86 exit; 87 fi 88#end if 89 90##note: validator for bed label 91#if $mode.mode_select == "multibed" 92 bedlabel=`echo $mode.label |awk '{print length(${dollar}0)}'` 93 if [[ ${dollar}bedlabel -gt 255 ]];then 94 echo "Bed Label exceed the limit of 255 characters!" ${gt}${ad}2; 95 exit; 96 fi 97 if [[ ${dollar}bedlabel -eq 0 ]];then 98 echo "Bed Label is required!" ${gt}${ad}2; 99 exit; 100 fi 101#end if 102 103lines=`wc -l $mode.bfile | tail -1 | awk '{print ${dollar}1}'` 104format=`$path/validation/fcfunc.py $mode.bfile` 105if [[ ${dollar}lines -gt 100000 ]];then 106 echo "BED file is too big! 100K lines are the maximum!" ${gt}${ad}2 107 exit; 108fi 109if [[ ${dollar}format != "passed" ]]; then 110 echo "Bed file 1: " ${dollar}format ${gt}${ad}2 111 exit; 112fi 113 114#if $mode.wfile.extension == "wig" 115#set $sitepro = "sitepro" 116#elif $mode.wfile.extension == "bigwig" 117#set $sitepro = "siteproBW" 118#end if 119 120#if $mode.mode_select == "single" 121##NOTE: cease, gca, and sitepro require python2.5 and above 122$sitepro -w $mode.wfile -b $mode.bfile --span=$span --pf-res=$pfres $dir --name=sitepro_out --dump ${ad}${gt} $log 123R --vanilla $lt sitepro_out.R ${ad}${gt}/dev/null 124mv sitepro_out.pdf $output 125cat *_dump.txt > $dump 126 127#elif $mode.mode_select == "multiwig" 128#set $tmp = "" 129#for $m in $mode.more 130#set $tmp = $tmp + "-w " +str($m.wig) + " -l " + str($m.label)+ " " 131#end for 132##NOTE: cease, gca, and sitepro require python2.5 and above 133 134$sitepro -w $mode.wfile -l $mode.label $tmp -b $mode.bfile --span=$span --pf-res=$pfres $dir --name=sitepro_out --dump ${ad}${gt} $log 135R --vanilla $lt sitepro_out.R ${ad}${gt}/dev/null 136mv sitepro_out.pdf $output 137cat *_dump.txt > $dump 138 139#elif $mode.mode_select == "multibed" 140#set $bedcount = 1 141#set $tmp = "" 142#for $m in $mode.more 143#set $bedcount = $bedcount + 1 144 lines=`wc -l $m.bfile | tail -1 | awk '{print ${dollar}1}'` 145 format=`$path/validation/fcfunc.py $m.bfile` 146 if [[ ${dollar}lines -gt 100000 ]];then 147 echo "BED file is too big! 100K lines are the maximum!" ${gt}${ad}2 148 exit; 149 fi 150 if [[ ${dollar}format != "passed" ]]; then 151 echo "Bed file ${bedcount}: " ${dollar}format ${gt}${ad}2 152 exit; 153 fi 154#set $tmp = $tmp + "-b " +str($m.bfile) + " -l " + str($m.label)+ " " 155#end for 156##NOTE: cease, gca, and sitepro require python2.5 and above 157 158 159$sitepro -w $mode.wfile -b $mode.bfile -l $mode.label $tmp --span=$span --pf-res=$pfres $dir --name=sitepro_out --dump ${ad}${gt} $log 160R --vanilla $lt sitepro_out.R ${ad}${gt}/dev/null 161mv sitepro_out.pdf $output 162cat *_dump.txt > $dump 163#end if 164 </configfile> 165 </configfiles> 166<tests> 167 <test maxseconds="3600" name="Sitepro_1"> 168 <param name="mode_select" value="single" /> 169 <param name="wfile" value="wiggle.wig" /> 170 <param name="bfile" value="bedfile.bed" /> 171 <param name="span" value="1000" /> 172 <param name="pfres" value="50" /> 173 <output name="output" file="sitepro_1/sitepro_1.pdf" /> 174 <output name="output" file="sitepro_1/sitepro_1.log" lines_diff = "200" /> 175 <output name="output" file="sitepro_1/sitepro_1_dump.txt" /> 176 </test> 177 <test maxseconds="3600" name="Sitepro_2"> 178 <param name="mode_select" value="single" /> 179 <param name="wfile" value="wiggle.wig" /> 180 <param name="bfile" value="bedfile.bed" /> 181 <param name="span" value="1000" /> 182 <param name="pfres" value="50" /> 183 <output name="output" file="sitepro_2/sitepro_2.pdf" /> 184 <output name="output" file="sitepro_2/sitepro_2.log" lines_diff = "200" /> 185 <output name="output" file="sitepro_2/sitepro_2_dump.txt" /> 186 </test> 187 <test maxseconds="3600" name="Sitepro_3"> 188 <param name="mode_select" value="single" /> 189 <param name="wfile" value="wiggle.wig" /> 190 <param name="bfile" value="bedfile.bed" /> 191 <param name="span" value="100" /> 192 <param name="pfres" value="10" /> 193 <output name="output" file="sitepro_3/sitepro_3.pdf" /> 194 <output name="output" file="sitepro_3/sitepro_3.log" lines_diff = "200" /> 195 <output name="output" file="sitepro_3/sitepro_3_dump.txt" /> 196 </test> 197 <test maxseconds="3600" name="Sitepro_4"> 198 <param name="mode_select" value="single" /> 199 <param name="wfile" value="wiggle.wig" /> 200 <param name="bfile" value="bedfile.bed" /> 201 <param name="span" value="100" /> 202 <param name="pfres" value="10" /> 203 <output name="output" file="sitepro_4/sitepro_4.pdf" /> 204 <output name="output" file="sitepro_4/sitepro_4.log" lines_diff = "200" /> 205 <output name="output" file="sitepro_4/sitepro_4_dump.txt" /> 206 </test> 207 <test maxseconds="3600" name="Sitepro_5"> 208 <param name="mode_select" value="single" /> 209 <param name="wfile" value="wiggle.wig" /> 210 <param name="bfile" value="bedfile.bed" /> 211 <param name="span" value="5000" /> 212 <param name="pfres" value="500" /> 213 <output name="output" file="sitepro_5/sitepro_5.pdf" /> 214 <output name="output" file="sitepro_5/sitepro_5.log" lines_diff = "200" /> 215 <output name="output" file="sitepro_5/sitepro_5_dump.txt" /> 216 </test> 217</tests> 218 <help> 219This tool draws the average score profile around given genomic 220sites. It's a module in CEAS package which is written by Hyunjin Gene 221Shin, published in Bioinformatics (pubmed id:19689956). 222 223.. class:: infomark 224 225**TIP #1:** If your query does not apper in the pulldown menu for BED Files, please convert your interval files to BED format. 226 227.. class:: infomark 228 229**TIP #2:** You can't use multiple BED files *AND* multiple Wiggle files as input. 230 231.. class:: infomark 232 233**TIP #3:** The tool can be used to check the signals of your ChIP 234sample around certain regions such as Transcription Start Sites, or 235Transcription Factor Binding Sites. 236 237.. class:: warningmark 238 239**NEED IMPROVEMENT** 240 241----- 242 243**Parameters** 244 245- **Sitepro behaviour mode** can only be '1 wiggle file against 1 BED 246 file', or 'multiple wiggle files against 1 BED file', or '1 wiggle 247 file against multiple BED files'. 248- **Wiggle label** When 'multi wiggle' mode is selected, you need to assign the labels for every wiggle files which will be shown in the final figure. 249- **BED label** When 'multi BED' mode is selected, you need to assign the labels for every BED files which will be shown in the final image. 250- **Span** is the distance from the center of each BED region in both directions(+/-) (eg, [c - span, c + span], where c is the center of a region). 251- **Profiling resolution** is the resolution to bin the scores in the final image. 252 253----- 254 255**script parameter list of Sitepro** 256 257Options: 258 --version show program's version number and exit 259 -h, --help Show this help message and exit. 260 -w WIG, --wig=WIG input WIG file. WARNING: both fixedStep and 261 variableStep WIG formats are accepted. Multiple WIG 262 files can be given via -w (--wig) individually (eg -w 263 WIG1.wig, -w WIG2.wig). WARNING! multiple wig and bed 264 files are not allowed. 265 -b BED, --bed=BED BED file of regions of interest. (eg, binding sites or 266 motif locations) Multiple BED files can be given via 267 -b (--bed) individually (eg -b BED1.bed -b BED2.bed). 268 WARNING! multiple wig and bed files are not allowed. 269 --span=SPAN Span from the center of each BED region in both 270 directions(+/-) (eg, [c - span, c + span], where c is 271 the center of a region), default:1000 bp 272 --pf-res=PF_RES Profiling resolution, default: 50 bp 273 --dir If set, the direction (+/-) is considered in 274 profiling. If no strand info given in the BED, this 275 option is ignored. 276 --dump If set, profiles are dumped as a TXT file 277 --name=NAME Name of this run. If not given, the body of the bed 278 file name will be used, 279 -l LABEL, --label=LABEL 280 Labels of the wig files. If given, they are used as 281 the legends of the plot and in naming the TXT files of 282 profile dumps; otherwise, the WIG file names will be 283 used as the labels. Multiple labels can be given via 284 -l (--label) individually (eg, -l LABEL1 -l LABEL2). 285 WARNING! The number and order of the labels must be 286 the same as the WIG files. 287 288----- 289 290**Output** 291 292- **PDF** format file. 293- Dumped signals within given intervals in **plain text**. 294 295 </help> 296 297</tool>