Mercurial > repos > vandelj > giant_aptsummarize

annotate galaxy/wrappers/ArrayNormalization.xml @ 0:708f43bda2b6 draft

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"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
author vandelj
date Fri, 26 Jun 2020 09:35:11 -0400
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children 2762a2622e0d
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708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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1 <tool name="GIANT-Normalization with APT Summarize" id="giant_aptsummarize" version="0.1.1">
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2 <description>Apply Affymetrix Power Tool summarize function to .CEL collection</description>
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3 <requirements>
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4 <requirement type="package" version="2.10.1">apt-probeset-summarize</requirement>
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5 </requirements>
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6 <stdio>
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7 <regex match="Execution halted"
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8 source="both"
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9 level="fatal"
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10 description="Execution halted, please contact tool developer or administrators." />
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11 <exit_code range="10" level="fatal" description="Error in post-treatments, see log file for more information." />
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12 <exit_code range="1:9" level="fatal" description="Error during apt command execution, see log file for more information." />
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13 </stdio>
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14
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17 <command> <![CDATA[
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18 ##ONLY FOR LOCAL TEST PURPOSE, COMMENT OTHERWISE
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19 ##set $pathToApt='/mnt/galaxy/home/galaxy/Software/ThermoFischer/apt-1.20.6-x86_64-intel-linux/bin'
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20
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21 mkdir ./apt_output/;
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22
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23 #if $mainCondition.arraySelection=="other":
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24 #if $CDFfile:
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25 ##.cdf file should has original name
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26 cp $CDFfile ./${CDFfile.name};
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27 #end if
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28 #end if
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29
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30
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31 ##run APT command
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32
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33 ##ONLY FOR LOCAL TEST PURPOSE COMMENT IF NOT NECESSARY
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34 ##${pathToApt}/apt-probeset-summarize -a $commandLine
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35 ##AND UNCOMMENT LINE BELOW
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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36 apt-probeset-summarize -a $commandLine
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37
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38 #if $mainCondition.arraySelection=="other":
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39 #if $PGFfile and $CLFfile:
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40 --use-pgf-names
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41 -p $PGFfile
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42 -c $CLFfile
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43 #end if
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44 #if $CDFfile:
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45 -d ./${CDFfile.name}
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46 #end if
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47 #if $MPSfile and $normLevel=="core":
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48 -m $MPSfile
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49 #end if
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50 #if $BGPfile:
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51 -b $BGPfile
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52 #end if
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53
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54 #else:
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55
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56 #if $mainCondition.arrayID.fields.pathPGF!="null" and $mainCondition.arrayID.fields.pathCLF!="null":
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57 --use-pgf-names
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58 -p $mainCondition.arrayID.fields.pathPGF
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59 -c $mainCondition.arrayID.fields.pathCLF
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60 #else:
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61 #if $mainCondition.arrayID.fields.pathCDF!="null":
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62 -d $mainCondition.arrayID.fields.pathCDF
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63 #end if
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64 #end if
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65 #if $normLevel=="core" and $mainCondition.arrayID.fields.pathMPS!="null":
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66 -m $mainCondition.arrayID.fields.pathMPS
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67 #end if
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68 #if $mainCondition.arrayID.fields.pathBGP!="null":
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69 -b $mainCondition.arrayID.fields.pathBGP
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70 #end if
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71 #end if
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72
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73 -o ./apt_output/
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74
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75 \$(echo '$inputData' | tr "," " ") >> $log 2>&1;
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76
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77 ret_code=\$?;
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78
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79 printf "[INFO]Normalized files: "$inputData >> $log;
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80
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81 if [ \$ret_code != 0 ]; then
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82 exit \$ret_code;
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83 else
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84
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85 ##launch post-treatment scripts
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86
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87 bash $scriptFormat;
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88 #if $annotationCondition.addAnnotation=="true":
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89 echo "[INFO]Annotation file used:" >> $log;
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90 #if $mainCondition.arraySelection=="other":
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91 bash $scriptAnnotation $mainCondition.annotationFile;
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92 echo $mainCondition.annotationFile.name >> $log;
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
93 #else:
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
94 #if $normLevel=="core":
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
95 bash $scriptAnnotation $mainCondition.arrayID.fields.pathAnnotTrans;
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
96 #else:
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
97 bash $scriptAnnotation $mainCondition.arrayID.fields.pathAnnotProbe;
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
98 #end if
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
99 cat $mainCondition.arrayID.fields.versionInfo >> $log;
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
100 #end if
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
101 #end if
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
102 fi;
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
103 printf "[INFO]End of tool script" >> $log;
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
104 ]]>
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
105 </command>
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
106
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
107
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
108
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
109 <configfiles>
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
110 <configfile name="scriptFormat">
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
111 <![CDATA[
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
112 #for $inputDataset in $inputData
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
113 echo '${inputDataset.name}' >> ./tempColumnName.txt
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
114 #end for
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
115 awk ' BEGIN{firstLine=1;OFS="";ORS=""} ARGIND==1{tab[FNR]=$1;nbCol=FNR} ARGIND==2 && !($1 ~ /\\#/){if(firstLine==0){print "\n"\$0}else{print "Conditions";for(i=1;i<=nbCol;i++){print "\t"tab[i]};firstLine=0}}' ./tempColumnName.txt ./apt_output/*summary.txt > $outputData
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
116
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
117 if [ ! -e $outputData ]; then
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
118 printf "[ERROR]Formating results failed" >> $log;
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
119 exit 10
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
120 fi
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
121 ]]>
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
122 </configfile>
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
123
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
124 <configfile name="scriptAnnotation">
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
125 <![CDATA[
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
126 #if $annotationCondition.addAnnotation=="true":
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
127 #if $annotationCondition.mergingMethod=="none":
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
128
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
129 #if $annotationCondition.keepAnnotated=="true":
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
130 awk 'BEGIN{OFS="\t"} ARGIND==1{dico[\$1]=\$2} ARGIND==2 && FNR==1{print \$0} ARGIND==2 && FNR>1{if(\$1 in dico){\$1=dico[\$1]"_("\$1")";print \$0}}' \$1 $outputData > ./tempData
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
131 #else:
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
132 awk 'BEGIN{OFS="\t"} ARGIND==1{dico[\$1]=\$2} ARGIND==2 && FNR==1{print \$0} ARGIND==2 && FNR>1{if(\$1 in dico){\$1=dico[\$1]"_("\$1")"};print \$0}' \$1 $outputData > ./tempData
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
133 #end if
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
134
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
135 #end if
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
136 #if $annotationCondition.mergingMethod=="mean":
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
137
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
138 #if $annotationCondition.keepAnnotated=="true":
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
139 awk 'BEGIN{OFS="\t"} ARGIND==1{dico[\$1]=\$2} ARGIND==2 && FNR==1{print \$0;nbCol=NF} ARGIND==2 && FNR>1{if(\$1 in dico){cpt[dico[\$1]]++;for(i=2;i<=nbCol;i++)sum[dico[\$1]][i]+=\$i}} END{for(iName in cpt){line=iName;for(iCol=2;iCol<=nbCol;iCol++){line=line"\t"sum[iName][iCol]/cpt[iName]};print line}}' \$1 $outputData > ./tempData
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
140 #else:
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
141 awk 'BEGIN{OFS="\t"} ARGIND==1{dico[\$1]=\$2} ARGIND==2 && FNR==1{print \$0;nbCol=NF} ARGIND==2 && FNR>1{if(\$1 in dico){cpt[dico[\$1]]++;for(i=2;i<=nbCol;i++)sum[dico[\$1]][i]+=\$i}else{print \$0}} END{for(iName in cpt){line=iName;for(iCol=2;iCol<=nbCol;iCol++){line=line"\t"sum[iName][iCol]/cpt[iName]};print line}}' \$1 $outputData > ./tempData
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
142 #end if
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
143
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
144 #end if
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
145
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
146 #if $annotationCondition.mergingMethod=="higherVar":
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
147
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
148 #if $annotationCondition.keepAnnotated=="true":
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
149 awk 'BEGIN{OFS="\t"} ARGIND==1{dico[\$1]=\$2} ARGIND==2 && FNR==1{print \$0;nbCol=NF} ARGIND==2 && FNR>1{if(\$1 in dico){mean=0;for(i=2;i<=nbCol;i++){mean+=\$i};mean=mean/(nbCol-1);curVar=0;for(i=2;i<=nbCol;i++){curVar+=(mean-\$i)^2};if(curVar>var[dico[\$1]]){var[dico[\$1]]=curVar;for(i=2;i<=nbCol;i++){bestVar[dico[\$1]][i]=\$i}}}} END{for(iName in bestVar){line=iName;for(iCol=2;iCol<=nbCol;iCol++){line=line"\t"bestVar[iName][iCol]};print line}}' \$1 $outputData > ./tempData
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
150 #else:
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
151 awk 'BEGIN{OFS="\t"} ARGIND==1{dico[\$1]=\$2} ARGIND==2 && FNR==1{print \$0;nbCol=NF} ARGIND==2 && FNR>1{if(\$1 in dico){mean=0;for(i=2;i<=nbCol;i++){mean+=\$i};mean=mean/(nbCol-1);curVar=0;for(i=2;i<=nbCol;i++){curVar+=(mean-\$i)^2};if(curVar>var[dico[\$1]]){var[dico[\$1]]=curVar;for(i=2;i<=nbCol;i++){bestVar[dico[\$1]][i]=\$i}}}else{print \$0}} END{for(iName in bestVar){line=iName;for(iCol=2;iCol<=nbCol;iCol++){line=line"\t"bestVar[iName][iCol]};print line}}' \$1 $outputData > ./tempData
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
152 #end if
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
153
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
154 #end if
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
155
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
156 #if $annotationCondition.mergingMethod=="lowerVar":
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
157
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
158 #if $annotationCondition.keepAnnotated=="true":
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
159 awk 'BEGIN{OFS="\t"} ARGIND==1{dico[\$1]=\$2} ARGIND==2 && FNR==1{print \$0;nbCol=NF} ARGIND==2 && FNR>1{if(\$1 in dico){mean=0;for(i=2;i<=nbCol;i++){mean+=\$i};mean=mean/(nbCol-1);curVar=0;for(i=2;i<=nbCol;i++){curVar+=(mean-\$i)^2};if(var[dico[\$1]]==0 || curVar<var[dico[\$1]]){var[dico[\$1]]=curVar;for(i=2;i<=nbCol;i++){bestVar[dico[\$1]][i]=\$i}}}} END{for(iName in bestVar){line=iName;for(iCol=2;iCol<=nbCol;iCol++){line=line"\t"bestVar[iName][iCol]};print line}}' \$1 $outputData > ./tempData
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
160 #else:
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
161 awk 'BEGIN{OFS="\t"} ARGIND==1{dico[\$1]=\$2} ARGIND==2 && FNR==1{print \$0;nbCol=NF} ARGIND==2 && FNR>1{if(\$1 in dico){mean=0;for(i=2;i<=nbCol;i++){mean+=\$i};mean=mean/(nbCol-1);curVar=0;for(i=2;i<=nbCol;i++){curVar+=(mean-\$i)^2};if(var[dico[\$1]]==0 || curVar<var[dico[\$1]]){var[dico[\$1]]=curVar;for(i=2;i<=nbCol;i++){bestVar[dico[\$1]][i]=\$i}}}else{print \$0}} END{for(iName in bestVar){line=iName;for(iCol=2;iCol<=nbCol;iCol++){line=line"\t"bestVar[iName][iCol]};print line}}' \$1 $outputData > ./tempData
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
162 #end if
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
163
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
164 #end if
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
165
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
166 if [ -e ./tempData ]; then
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
167 mv -f ./tempData $outputData
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
168 else
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
169 printf "[ERROR]Annotation merge failed" >> $log;
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
170 exit 10
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
171 fi
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172
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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173 #end if
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174
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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175 ]]>
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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176 </configfile>
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177 </configfiles>
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178
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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179
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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180
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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181 <inputs>
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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182 <param type="text" name="title" value="APT_toPersonalize" label="Title for output"/>
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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183
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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184 <param type="data" name="inputData" format="cel" label=".cel collection file" optional="false" multiple="true">
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185 <validator type="empty_dataset" message="At least one data file should be selected"></validator>
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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186 </param>
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187
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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188 <param type="select" name="commandLine" display="radio" label="Normalization to perform" help="For more details go to APT webpage">
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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189 <option value="rma-gc-scale" selected="true">gc correction + scale intensity + rma</option>
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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190 <option value="scale-intensities,rma-bg,quant-norm.sketch=0.usepm=true.bioc=true,pm-only,med-polish">scale intensity + rma</option>
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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191 <option value="gc-correction,rma-bg,quant-norm.sketch=0.usepm=true.bioc=true,pm-only,med-polish">gc correction + rma</option>
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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192 <option value="rma">rma</option>
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193 </param>
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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194
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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195 <param type="select" name="normLevel" display="radio" label="Normalization level" help="'Core genes' option is not available for all arrays">
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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196 <option value="core">Core genes</option>
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197 <option value="probeset">Probe set</option>
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198 </param>
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199
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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200 <conditional name="mainCondition">
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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201
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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202 <param name="arraySelection" type="select" label="Select GeneChip array configuration files">
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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203 <option value="common">pre-loaded array files</option>
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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204 <option value="other">array files selection</option>
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205 </param>
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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206
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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207 <when value="common">
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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208 <param name="arrayID" label="Name" type="select">
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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209 <options from_data_table="aptTool">
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210 </options>
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211 </param>
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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212 </when>
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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213
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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214 <when value="other">
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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215
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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216 <param type="data" format="data" name="PGFfile" label=".pgf indicates which probes are grouped together into a probeset*" optional="true" multiple="false">
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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217 </param>
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218
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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219 <param type="data" format="data" name="CLFfile" label=".clf indicates where the probes are located in the CEL file*" optional="true" multiple="false">
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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220 </param>
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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221
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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222 <param type="data" format="data" name="CDFfile" label=".cdf contains both .pgf and .clf informations* (requested only if .pgf and .clf files are not available)" optional="true" multiple="false">
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223 </param>
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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224
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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225 <param type="data" format="data" name="MPSfile" label=".mps defines a probeset as a collection of existing probesets* (requested for normalization at gene level)" optional="true" multiple="false" help="If .mps is not selected/available a 'probeset level' normalization will be automatically performed">
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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226 </param>
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227
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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228 <param type="data" format="data" name="BGPfile" label=".bgp indicates which probes are to be used for computing background* (requested only if GC driven background correction is applied)" optional="true" multiple="false" help="*Files should be downloaded from corresponding array specific Affymetrix webpage to insure format compatibility">
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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229 </param>
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230
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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231 <param type="data" name="annotationFile" format="tabular" label="tabular file containing available probesets annotation (requested if annotation options are selected)" optional="true" multiple="false" >
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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232 </param>
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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233
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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234 </when>
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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235 </conditional>
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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236
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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237 <conditional name="annotationCondition">
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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238 <param type="boolean" name="addAnnotation" checked="false" label="Add gene annotation">
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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239 </param>
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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240 <when value="true">
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241 <param type="boolean" name="keepAnnotated" checked="false" label="Discard probe set without gene annotation">
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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242 </param>
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243
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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244 <param type="select" name="mergingMethod" display="radio" label="Merging approach for probe set with same gene annotation">
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245 <option value="none">No merging</option>
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246 <option value="mean" selected="true">Mean between probes [recommended]</option>
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247 <option value="higherVar">Keep probe with higher variance</option>
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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248 <option value="lowerVar">Keep probe with lower variance</option>
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249 </param>
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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250 </when>
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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251 <when value="false">
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252 </when>
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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253 </conditional>
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254 </inputs>
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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255
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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256
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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257
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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258 <outputs>
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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259 <data format="tabular" name="outputData" label="${title}_NormalizedData"/>
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260 <data format="txt" name="log" label="${title}_Log" />
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261 </outputs>
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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262
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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263
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264
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265 <tests>
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266 <test maxseconds="3600">
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267 <param name="inputData" value="./CELfiles/GSM205766.CEL,./CELfiles/GSM205767.CEL,./CELfiles/GSM205768.CEL" />
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268 <param name="commandLine" value="rma-gc-scale" />
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269 <param name="normLevel" value="core" />
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270 <param name="arraySelection" value="other" />
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271 <param name="CDFfile" value="./Mouse430_2.cdf" />
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272 <param name="annotationFile" value="./formatedAnnotation.csv" />
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273 <param name="addAnnotation" value="true" />
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274 <param name="keepAnnotated" value="false" />
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275 <param name="mergingMethod" value="mean" />
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276 <output name="outputData" file="./APT-summarize/expressionOutput.csv" />
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277 <output name="log" file="./APT-summarize/output.log" lines_diff="2" />
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278 </test>
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279 </tests>
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280
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281
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282
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283
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284 <help>
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285 <![CDATA[
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286 **What it does**
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287
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288 To normalize expression data from Affymetrix GeneChip arrays through Affymetrix Power Tools software.
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289
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290 -----
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291
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292 **Parameters**
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293
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294 \- **Title** to personalize output file names (please avoid special characters).
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295
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296
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297 \- **.CEL files** you want to normalize (you can select multiple .CEL files or unique collection).
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298
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299
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300 \- **Analysis to perform** : as this tool run the 'apt-probeset-summarize' command line from Affymetrix Power Tool software, this field represents the desired analysis pathway (-a parameter). Analysis pathways are summarized through predifined pathway alias with full description of all run steps below:
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301
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302 - gc correction + scale intensity + rma: "gc-correction,scale-intensities,rma-bg,quant-norm.sketch=0.usepm=true.bioc=true,pm-only,med-polish"
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303
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304 - scale intensity + rma: "scale-intensities,rma-bg,quant-norm.sketch=0.usepm=true.bioc=true,pm-only,med-polish"
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305
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306 - gc correction + rma: "gc-correction,rma-bg,quant-norm.sketch=0.usepm=true.bioc=true,pm-only,med-polish"
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307
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308 - rma: "rma-bg,quant-norm.sketch=0.usepm=true.bioc=true,pm-only,med-polish"
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309
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310 Please refer to `APT tool web page`__ to get more details about analysis steps.
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311
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312 \- **Normalization level** to choose when GeneChip array kind allows such distinction (ie. when a .mps file exists in Affymetrix webpage). 'Probe set level' is the first level where probes for same exon are merged in probe sets. 'Gene level' [recommended] is an upper level where several probe sets are merged in meta probe sets. If a meta probe set can be see as a good single gene expression indicator, several meta probe sets can still share same gene annotation.
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313
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314 \- **GeneChip array configuration files** according to .CEL files. Configuration files for given arrays can be pre-loaded by administrators of the used Galaxy instance and listed in the aptTool.loc file. In this case you just have to select the array kind according to .CEL files, thus pre-loaded configuration files will be used automatically for normalization. If configuration files were not pre-loaded, you have to choose "array files selection" and then select manually configuration files for the corresponding array. Configuration files (.pgf, .clf, .cdf, .mps, .bgp) are available in library archive files from the Affymetrix webpage of the array (as an example, configuration files for HTA2.0 array are found in the 'Main Analysis Files' in the 'Support file' section of `this page`__). All these files are not mandatory for all normalizations. For basic normalization, both .pgf and.clf files or only .cdf file are mandatory. .mps file is requested for gene level normalization if it is available (see Normalization level parameter). .bgp file is requested for analysis pathway with specific background computation. Annotation file is a simple two column tabular file, with first column containing probe set names and second corresponding annotations, it should not contains any column header. This file can be generated from Affymetrix annotation file available in the same section as array configuration files in Affymetrix webpages, please keep a trace of used annotation version to insure reproducibility.
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315
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316 Extract of annotation file::
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317
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318 TC01000020.hg.1 SAMD11
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319 TC01000021.hg.1 KLHL17
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320 TC01000022.hg.1 PLEKHN1
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321 TC01000023.hg.1 ISG15
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322 TC01000024.hg.1 AGRN
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323
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324 \- **Gene annotation** : add gene annotation when available (for pre-loaded arrays, annotation file path should be filled in the aptTool.loc file, for other arrays, annotation file should be selected manually). You can choose to keep or discard in normalized file (meta) probe sets without match in annotation file and select merging policy for probe sets sharing same gene annotation.
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325
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326 -----
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327
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328 **Advanced parameters**
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329
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330 \- **Additional parameter** to give to 'apt-probeset-summarize' command line except -a, -o, -d, -p, -c, -m, -b parameters already filled by previous fields.
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331
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332 -----
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333
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334 **Outputs**
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335
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336 \- **tabular file** containing log2 transformed normalized data as tab delimited matrix. First row contains .CEL names and first column contains (meta) probe set names and/or annotated gene names::
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337
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338 Conditions 157_(HuGene-2_0-st).CEL 156_(HuGene-2_0-st).CEL 155_(HuGene-2_0-st).CEL 154_(HuGene-2_0-st).CEL
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339 DDX11L2 4.500872 4.429759 4.780281 4.996189
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340 MIR1302-2 3.415065 3.520472 3.471503 3.567988
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341 OR4F5 3.737956 3.011586 3.424494 3.497545
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342 VWA1 5.189621 5.129595 4.806793 5.227014
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343
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344 \- **LOG file** containing information about execution. Useful especially if tool execution fais. Please attach this log file in any bug report.
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345
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346 .. __: http://media.affymetrix.com/support/developer/powertools/changelog/apt-probeset-summarize.html#intro
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347
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348 .. __: https://www.thermofisher.com/order/catalog/product/902233#/902233
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349
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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350 ]]>
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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351 </help>
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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352
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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353
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354 <citations>
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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355 <citation type="bibtex">@misc{vandel_jimmy_2018_1477870, author = {Vandel, J. and Gheeraert, C. and Eeckhoute, J. and Staels, B. and Lefebvre, P. and Dubois-Chevalier, J.}, title = {GIANT: Galaxy-based Interactive tools for ANalaysis of Transcriptomic data}, month = nov, year = 2018, doi = {10.5281/zenodo.1477870}, url = {https://doi.org/10.5281/zenodo.1477870}
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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356 }</citation>
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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357
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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358 <citation type="bibtex">@online{apt, author = {Thermo Fisher Scientific}, title = {Affymetrix Power Tools}, publisher = {Life Technologies Corp.}, address = {USA, MA}, version = {2.10.2}, year = {2018}, url = {https://www.affymetrix.com/support/developer/powertools/changelog/index.html}
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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359 }</citation>
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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360 </citations>
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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361 </tool>