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changeset 8:53846f74a019 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit ef11594cf3ca79e444ab4e30d83de5951a636faf
author iuc
date Sun, 10 Jul 2016 09:02:14 -0400
parents b3f7ff168b9a
children 40b8472e91ca
files fimo.xml test-data/fimo_output_html_1.html test-data/fimo_output_html_2.html test-data/fimo_output_xml_1.xml test-data/fimo_output_xml_2.xml test-data/meme_input_1.fasta test-data/meme_output_html_1.html test-data/meme_output_html_2.html test-data/meme_output_txt_1.txt test-data/meme_output_txt_2.txt test-data/meme_output_xml_1.xml test-data/meme_output_xml_2.xml test-data/prior30.plib tool_dependencies.xml
diffstat 14 files changed, 368 insertions(+), 20 deletions(-) [+]
line wrap: on
line diff
--- a/fimo.xml	Thu Jul 07 09:55:00 2016 -0400
+++ b/fimo.xml	Sun Jul 10 09:02:14 2016 -0400
@@ -1,9 +1,16 @@
-<tool id="meme_fimo" name="FIMO" version="4.11.0.4">
+<tool id="meme_fimo" name="FIMO" version="4.11.1.0">
     <description>- Scan a set of sequences for motifs.</description>
     <requirements>
-        <requirement type="package" version="6.9.3">imagemagick</requirement>
-        <requirement type="package" version="4.11.0">meme</requirement>
+        <requirement type="package" version="1.3.20">graphicsmagick</requirement>
+        <requirement type="package" version="4.11.1">meme</requirement>
     </requirements>
+    <stdio>
+        <!-- Anything other than zero is an error -->
+        <exit_code range="1:" />
+        <!-- In case the return code has not been set propery check stderr too -->
+        <regex match="Error:" />
+        <regex match="Exception:" />
+    </stdio>
     <command>
         <![CDATA[
             mkdir -p output &&
@@ -255,7 +262,7 @@
             <param name="fasta_type_selector" value="history"/>
             <param name="input_database" value="phiX.fasta" ftype="fasta"/>
             <param name="options_type_selector" value="advanced"/>
-            <param name="parse_genomic_coord" value="--parse_genomic_coord"/>
+            <param name="parse_genomic_coord" value="yes"/>
             <param name="remove_duplicate_coords" value="yes"/>
             <param name="output_separate_motifs" value="yes"/>
             <param name="non_commercial_use" value="True"/>
--- a/test-data/fimo_output_html_1.html	Thu Jul 07 09:55:00 2016 -0400
+++ b/test-data/fimo_output_html_1.html	Sun Jul 10 09:02:14 2016 -0400
@@ -25,7 +25,7 @@
 <center><big><b>FIMO - Motif search tool</b></big></center>
 <hr>
 <p>
-FIMO version 4.11.0, (Release date: Thu Nov 26 17:48:49 2015 +1000)
+FIMO version 4.11.1, (Release date: Fri Jan 15 12:51:59 2016 -0800)
 </p>
 <p>
 For further information on how to interpret these results
--- a/test-data/fimo_output_html_2.html	Thu Jul 07 09:55:00 2016 -0400
+++ b/test-data/fimo_output_html_2.html	Sun Jul 10 09:02:14 2016 -0400
@@ -25,7 +25,7 @@
 <center><big><b>FIMO - Motif search tool</b></big></center>
 <hr>
 <p>
-FIMO version 4.11.0, (Release date: Thu Nov 26 17:48:49 2015 +1000)
+FIMO version 4.11.1, (Release date: Fri Jan 15 12:51:59 2016 -0800)
 </p>
 <p>
 For further information on how to interpret these results
--- a/test-data/fimo_output_xml_1.xml	Thu Jul 07 09:55:00 2016 -0400
+++ b/test-data/fimo_output_xml_1.xml	Sun Jul 10 09:02:14 2016 -0400
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <!-- Begin document body -->
-<fimo version="4.11.0" release="Thu Nov 26 17:48:49 2015 +1000">
+<fimo version="4.11.1" release="Fri Jan 15 12:51:59 2016 -0800">
   xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
   xsi:schemaLocation=  xmlns:fimo="http://noble.gs.washington.edu/schema/fimo"
 >
--- a/test-data/fimo_output_xml_2.xml	Thu Jul 07 09:55:00 2016 -0400
+++ b/test-data/fimo_output_xml_2.xml	Sun Jul 10 09:02:14 2016 -0400
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <!-- Begin document body -->
-<fimo version="4.11.0" release="Thu Nov 26 17:48:49 2015 +1000">
+<fimo version="4.11.1" release="Fri Jan 15 12:51:59 2016 -0800">
   xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
   xsi:schemaLocation=  xmlns:fimo="http://noble.gs.washington.edu/schema/fimo"
 >
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/meme_input_1.fasta	Sun Jul 10 09:02:14 2016 -0400
@@ -0,0 +1,66 @@
+>chr21_19617074_19617124_+
+AAAAATTATTACTAGGGAGGGGGCCGGAACCTCGGGACGTGGGTATATAA
+>chr21_26934381_26934431_+
+GCGCCTGGTCGGTTATGAGTCACAAGTGAGTTATAAAAGGGTCGCACGTT
+>chr21_28217753_28217803_-
+CAAAGGGGAGGAGTGGGGTGGGGGTGGGGGTTTCACTGGTCCACTATAAA
+>chr21_31710037_31710087_-
+AACACCCAGGTTTCTGAGTATATAATCGCCGCACCAAAGAATTTAATTTT
+>chr21_31744582_31744632_-
+CCCAGGTCTAAGAGCATATATAACTTGGAGTCCAGACTATGACATTCAAA
+>chr21_31768316_31768366_+
+AACGTATATAAATGGTCCTGTCCAGATGTGGCATGCAAACTCAGAATCTT
+>chr21_31914206_31914256_-
+TGACACCCACTACTTAGAGTATAAAATCATTCTGAGAAGTTAGAGACACC
+>chr21_31933633_31933683_-
+TCAGAGTATATATAAATGTTCCTGTCCAGTCACAGTCACCAAACTGACCT
+>chr21_31962741_31962791_-
+ACATATAACTCAGGTTGGATAAAATAATTTGTACAAATCAGGAGAGTCAA
+>chr21_31964683_31964733_+
+TCTGATTCACTGAGGCATATAAAAGGCCCTCTGCGGAGAAGTGTCCATAC
+>chr21_31973364_31973414_+
+aaacttaaaactctataaacttaaaactCTAGAATCTGATCCTGCTATAC
+>chr21_31992870_31992920_+
+CTCATACACTATTGAAGATGTATAAAATTTCATTTGCAGATGGTGACATT
+>chr21_32185595_32185645_-
+TCACCACCCACCAGAGCTGGGATATATAAAGAAGGTTCTGAGACTAGGAA
+>chr21_32202076_32202126_-
+TGCCCACCAGCTTGAGGTATAAAAAGCCCTGTACGGGAAGAGACCTTCAT
+>chr21_32253899_32253949_-
+AGCCCCACCCACCAGCAAGGATATATAAAAGCTCAGGAGTCTGGAGTGAC
+>chr21_32410820_32410870_-
+TCTACCCCACTAATCACTGAGGATGTATAAAAGTCCCAGGGAAGCTGGTG
+>chr21_36411748_36411798_-
+ATAGTTCTGTATAGTTTCAGTTGGCATCtaaaaattatataactttattt
+>chr21_37838750_37838800_-
+gatggttttataaggggcctcaccctcggctcagccctcattcttctcct
+>chr21_45705687_45705737_+
+CCGGGGCGGAGCGGCCTTTGCTCTTTGCGTGGTCGCGGGGGTATAACAGC
+>chr21_45971413_45971463_-
+CAGGCCCTGGGCATATAAAAGCCCCAGCAGCCAACAGGctcacacacaca
+>chr21_45978668_45978718_-
+CAGAGGGGTATAAAGGTTCCGACCACTCAGAGGCCTGGCACGAtcactca
+>chr21_45993530_45993580_+
+CCAAGGAGGAGTATAAAAGCCCCACAAACCCGAGCACCTCACTCACTCGC
+>chr21_46020421_46020471_+
+GAGACATATAAAAGCCAACATCCCTGAGCACCTAACACACGGactcactc
+>chr21_46031920_46031970_+
+GGAAAATACCCAGGGAGGGTATAAAACCTCAGCAGCCAGGGCACACAAAC
+>chr21_46046964_46047014_+
+ACAAGGCCAGGAGGGGTATAAAAGCCTGAGAGCCCCAAGAACctcacaca
+>chr21_46057197_46057247_+
+ATTGCTGAGTCTCCTGCTGGGAAAACACAGGCCCTGGGCATATAAAAGCC
+>chr21_46086869_46086919_-
+GACAGGTGTGCTTCTGTGCTGTGGGGATGCCTGGGCCCAGGTATAAAGGC
+>chr21_46102103_46102153_-
+AGGTGTGTGCTTCTGTGCTGTGGGGATGCCTGGGTCCAGGTATAAAGGCT
+>chr21_47517957_47518007_+
+CCTGGCGGCGGGGCGGGTCAGGCCGGCGGGGCGGGGTATAAAGGGGGCGG
+>chr21_47517957_47518007_+
+CCTGGCGGCGGGGCGGGTCAGGCCGGCGGGGCGGGGTATAAAGGGGGCGG
+>chr21_47517957_47518007_+
+CCTGGCGGCGGGGCGGGTCAGGCCGGCGGGGCGGGGTATAAAGGGGGCGG
+>chr21_47575506_47575556_-
+TGAGAAGCCGGTGGGGAGGTGCTGCCGGTGAGCGTATAAAGGCCCTGGCG
+>chr21_47575506_47575556_-
+TGAGAAGCCGGTGGGGAGGTGCTGCCGGTGAGCGTATAAAGGCCCTGGCG
--- a/test-data/meme_output_html_1.html	Thu Jul 07 09:55:00 2016 -0400
+++ b/test-data/meme_output_html_1.html	Sun Jul 10 09:02:14 2016 -0400
@@ -7,8 +7,8 @@
       // @JSON_VAR data
       var data = {
         "program": "MEME",
-        "version": "4.11.0",
-        "release": "Thu Nov 26 17:48:49 2015 +1000",
+        "version": "4.11.1",
+        "release": "Fri Jan 15 12:51:59 2016 -0800",
         "stop_reason": "Stopped because requested number of motifs (1) found.",
         "cmd": [
           "meme",
--- a/test-data/meme_output_html_2.html	Thu Jul 07 09:55:00 2016 -0400
+++ b/test-data/meme_output_html_2.html	Sun Jul 10 09:02:14 2016 -0400
@@ -7,8 +7,8 @@
       // @JSON_VAR data
       var data = {
         "program": "MEME",
-        "version": "4.11.0",
-        "release": "Thu Nov 26 17:48:49 2015 +1000",
+        "version": "4.11.1",
+        "release": "Fri Jan 15 12:51:59 2016 -0800",
         "stop_reason": "Stopped because requested number of motifs (1) found.",
         "cmd": [
           "meme",
--- a/test-data/meme_output_txt_1.txt	Thu Jul 07 09:55:00 2016 -0400
+++ b/test-data/meme_output_txt_1.txt	Sun Jul 10 09:02:14 2016 -0400
@@ -1,7 +1,7 @@
 ********************************************************************************
 MEME - Motif discovery tool
 ********************************************************************************
-MEME version 4.11.0 (Release date: Thu Nov 26 17:48:49 2015 +1000)
+MEME version 4.11.1 (Release date: Fri Jan 15 12:51:59 2016 -0800)
 
 For further information on how to interpret these results or to get
 a copy of the MEME software please access http://meme-suite.org .
--- a/test-data/meme_output_txt_2.txt	Thu Jul 07 09:55:00 2016 -0400
+++ b/test-data/meme_output_txt_2.txt	Sun Jul 10 09:02:14 2016 -0400
@@ -1,7 +1,7 @@
 ********************************************************************************
 MEME - Motif discovery tool
 ********************************************************************************
-MEME version 4.11.0 (Release date: Thu Nov 26 17:48:49 2015 +1000)
+MEME version 4.11.1 (Release date: Fri Jan 15 12:51:59 2016 -0800)
 
 For further information on how to interpret these results or to get
 a copy of the MEME software please access http://meme-suite.org .
--- a/test-data/meme_output_xml_1.xml	Thu Jul 07 09:55:00 2016 -0400
+++ b/test-data/meme_output_xml_1.xml	Sun Jul 10 09:02:14 2016 -0400
@@ -161,7 +161,7 @@
 
 ]>
 <!-- Begin document body -->
-<MEME version="4.11.0" release="Thu Nov 26 17:48:49 2015 +1000">
+<MEME version="4.11.1" release="Fri Jan 15 12:51:59 2016 -0800">
 <training_set datafile="/Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2490.dat" length="30">
 <alphabet name="Protein" like="protein">
 <letter id="A" symbol="A" name="Alanine" colour="0000CC"/>
--- a/test-data/meme_output_xml_2.xml	Thu Jul 07 09:55:00 2016 -0400
+++ b/test-data/meme_output_xml_2.xml	Sun Jul 10 09:02:14 2016 -0400
@@ -161,7 +161,7 @@
 
 ]>
 <!-- Begin document body -->
-<MEME version="4.11.0" release="Thu Nov 26 17:48:49 2015 +1000">
+<MEME version="4.11.1" release="Fri Jan 15 12:51:59 2016 -0800">
 <training_set datafile="Galaxy_FASTA_Input" length="30">
 <alphabet name="DNA" like="dna">
 <letter id="A" symbol="A" complement="T" name="Adenine" colour="CC0000"/>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/prior30.plib	Sun Jul 10 09:02:14 2016 -0400
@@ -0,0 +1,275 @@
+Alphabet= ACDEFGHIKLMNPQRSTVWY
+NumDistr= 30
+Number= 0
+Mixture= 0.055795
+B= 5.623820
+Alpha= 0.0855491 0.0221831 0.0111063 0.0209959 0.0505726 0.025437 0.0155389 0.132951 0.0247865 0.150287 0.0577239 0.0209317 0.0166629 0.0220905 0.0244295 0.0497608 0.070277 0.157532 0.0102219 0.0309633 
+FullUpdate= 1
+QUpdate= 1
+StructID=      0
+Comment=    HMM9.4 reestimated in henikoff29.2
+
+Number= 1
+Mixture= 0.198333
+B= 0.097240
+Alpha= 0.0562629 0.0329597 0.0692513 0.0385232 0.0400041 0.143573 0.0428939 0.0226244 0.0442102 0.0665467 0.0117853 0.0447655 0.0833299 0.0395825 0.0611271 0.0588852 0.0513472 0.0317153 0.0237865 0.0368161 
+FullUpdate= 1
+QUpdate= 1
+StructID=       24
+Comment=      Outside
+
+Number= 2
+Mixture= 0.043566
+B= 1.648336
+Alpha= 0.0144564 0.00845337 0.00785519 0.00864933 0.255959 0.0110815 0.0509526 0.0234533 0.0120443 0.0561967 0.015111 0.0190974 0.00857653 0.0167812 0.0164918 0.0197108 0.0151013 0.0252782 0.050139 0.364613 
+FullUpdate= 1
+QUpdate= 1
+StructID=       26
+Comment=       Inside
+
+Number= 3
+Mixture= 0.060170
+B= 2.595432
+Alpha= 0.0452144 0.00587917 0.169731 0.0751478 0.00749471 0.0845832 0.0369819 0.00610072 0.0548186 0.011029 0.00382749 0.212785 0.0206532 0.0416705 0.0280716 0.117267 0.0533742 0.00943157 0.00216149 0.0137784 
+FullUpdate= 1
+QUpdate= 1
+StructID=       19
+Comment=      Outside Alpha
+
+Number= 4
+Mixture= 0.065466
+B= 3.112271
+Alpha= 0.0361167 0.0049157 0.0134924 0.0461325 0.00557631 0.0209043 0.0302551 0.016425 0.307554 0.0338255 0.0139435 0.0360733 0.0127659 0.0873761 0.222668 0.0369042 0.0354442 0.0228891 0.00434827 0.0123906 
+FullUpdate= 1
+QUpdate= 1
+StructID=       21
+Comment=       Outside Beta
+
+Number= 5
+Mixture= 0.067614
+B= 2.053644
+Alpha= 0.0194362 0.00765176 0.00188738 0.00372898 0.0849894 0.00421787 0.00400459 0.152735 0.00407958 0.4568 0.106051 0.00304386 0.00545956 0.00900935 0.00605071 0.00519029 0.016255 0.0861045 0.00787965 0.0154248 
+FullUpdate= 1
+QUpdate= 1
+StructID=       22
+Comment=      Inside alpha
+
+Number= 6
+Mixture= 0.080724
+B= 2.138987
+Alpha= 0.0423172 0.0153891 0.00409306 0.00565735 0.0197117 0.00590607 0.00139926 0.307863 0.00544884 0.115721 0.0285808 0.00522771 0.00474851 0.00328193 0.00351054 0.00892385 0.0348922 0.380003 0.00117673 0.00614917 
+FullUpdate= 1
+QUpdate= 1
+StructID=       23
+Comment=       Inside beta
+
+Number= 7
+Mixture= 0.051030
+B= 3.878926
+Alpha= 0.0548123 0.000759746 0.144127 0.46019 0.00249502 0.0192754 0.0106535 0.00938765 0.0562429 0.0163148 0.00717389 0.0245612 0.0177482 0.0744802 0.0199233 0.0323535 0.0257651 0.018574 0.00087086 0.00429088 
+FullUpdate= 1
+QUpdate= 1
+StructID=       23
+Comment=      Alpha helix
+
+Number= 8
+Mixture= 0.103529
+B= 1.486325
+Alpha= 0.315754 0.0384546 0.0116388 0.0133665 0.0111126 0.107921 0.00752325 0.0154885 0.0111281 0.0231087 0.011626 0.0228375 0.0304785 0.0166632 0.0156345 0.186379 0.0954421 0.0546691 0.00351538 0.00725682 
+FullUpdate= 1
+QUpdate= 1
+StructID=       23
+Comment=      Beta strand
+
+Number= 9
+Mixture= 0.062940
+B= 8.221215
+Alpha= 0.0869919 0.00672577 0.0600995 0.10763 0.0153489 0.0378086 0.0325335 0.023388 0.113765 0.041623 0.0196906 0.0625344 0.0262599 0.0788667 0.0707399 0.0886634 0.0666777 0.0361472 0.00484308 0.0196629 
+FullUpdate= 1
+QUpdate= 1
+StructID=       23
+Comment=      Other
+
+Number= 10
+Mixture= 0.012518
+B= 38.955631
+Alpha= 0.732922 0.0145131 0.00623235 0.00951423 0.00717778 0.0289521 0.00351664 0.0125081 0.00886593 0.0183651 0.00832812 0.00670968 0.00364556 0.00622169 0.00812899 0.0582399 0.0205067 0.0394327 0.00207485 0.00414489 
+FullUpdate= 1
+QUpdate= 1
+StructID=      0
+Comment=      A
+
+Number= 11
+Mixture= 0.004953
+B= 381.562195
+Alpha= 0.00563239 0.959814 0.00144129 0.00213042 0.00158645 0.00168393 0.000989765 0.00325263 0.00148501 0.00343924 0.00168673 0.00159054 0.00121534 0.00129942 0.00195209 0.00296106 0.0039912 0.00266944 0.000327808 0.000851203 
+FullUpdate= 1
+QUpdate= 1
+StructID=      0
+Comment=      C
+
+Number= 12
+Mixture= 0.013849
+B= 90.727570
+Alpha= 0.00897115 0.00169015 0.859473 0.0360829 0.00269485 0.00606504 0.00469816 0.00400134 0.0047981 0.00514968 0.00208395 0.029754 0.00241276 0.0045506 0.00433816 0.0088208 0.00511143 0.00527448 0.00104469 0.00298475 
+FullUpdate= 1
+QUpdate= 1
+StructID=      0
+Comment=     D 
+
+Number= 13
+Mixture= 0.008388
+B= 404.591034
+Alpha= 0.00241514 0.000413991 0.0122981 0.96369 0.000665578 0.00187461 0.00106904 0.00149214 0.00121548 0.00129791 0.000554145 0.00253496 0.000624495 0.00316839 0.00115045 0.00171781 0.001468 0.0014564 0.000278652 0.000614791 
+FullUpdate= 1
+QUpdate= 1
+StructID=      0
+Comment=      E 
+
+Number= 14
+Mixture= 0.008064
+B= 83.323669
+Alpha= 0.00839779 0.00428348 0.00298116 0.00358128 0.850936 0.00329382 0.00196832 0.0130534 0.00320345 0.0351883 0.00729724 0.00287304 0.00358482 0.00218728 0.00264753 0.00833798 0.00418729 0.0120684 0.00448366 0.025446 
+FullUpdate= 1
+QUpdate= 1
+StructID=      0
+Comment=     F 
+
+Number= 15
+Mixture= 0.032205
+B= 32.644871
+Alpha= 0.0234448 0.00236512 0.0112957 0.00811395 0.00248143 0.868718 0.00345598 0.00342985 0.00859682 0.0040966 0.00239339 0.012342 0.00423123 0.00440054 0.00795347 0.0165095 0.0065024 0.00550512 0.00140604 0.00275817 
+FullUpdate= 1
+QUpdate= 1
+StructID=      0
+Comment=     G 
+
+Number= 16
+Mixture= 0.005033
+B= 35.520824
+Alpha= 0.0100058 0.00386024 0.0131498 0.0108984 0.0122851 0.00738691 0.722249 0.00521193 0.00686054 0.0150103 0.00673014 0.0367074 0.00625526 0.0429912 0.0234127 0.0187246 0.0128445 0.00837399 0.00390723 0.0331349 
+FullUpdate= 1
+QUpdate= 1
+StructID=      0
+Comment=     H 
+
+Number= 17
+Mixture= 0.007454
+B= 101.265472
+Alpha= 0.0106938 0.00267663 0.00404166 0.00466637 0.00838963 0.00372808 0.00182575 0.681615 0.0059102 0.0770333 0.0184335 0.004676 0.0027124 0.00372663 0.00418165 0.00773357 0.0109237 0.140679 0.00140417 0.00494911 
+FullUpdate= 1
+QUpdate= 1
+StructID=      0
+Comment=     I 
+
+Number= 18
+Mixture= 0.009400
+B= 150.415985
+Alpha= 0.00688657 0.00169711 0.00222738 0.00346887 0.00115861 0.00302866 0.00209171 0.00400905 0.903944 0.0037747 0.00186061 0.00449531 0.00249618 0.00324487 0.041775 0.00392196 0.00461714 0.00296607 0.000893256 0.00144282 
+FullUpdate= 1
+QUpdate= 1
+StructID=      0
+Comment=      K 
+
+Number= 19
+Mixture= 0.017057
+B= 31.896633
+Alpha= 0.0114646 0.00367926 0.00296188 0.00596126 0.0190009 0.00382486 0.00338381 0.0401936 0.00650072 0.790038 0.031659 0.00392791 0.0050046 0.00753591 0.00771818 0.00748621 0.0101555 0.0312597 0.00242405 0.00581952 
+FullUpdate= 1
+QUpdate= 1
+StructID=      0
+Comment=     L 
+
+Number= 20
+Mixture= 0.002761
+B= 201.346268
+Alpha= 0.00353933 0.00165628 0.0014931 0.00161065 0.00279831 0.00194259 0.00101868 0.00969101 0.00211316 0.0217036 0.928022 0.00162899 0.0015681 0.0015629 0.00138977 0.00294601 0.00311476 0.00723178 0.00156295 0.00340569 
+FullUpdate= 1
+QUpdate= 1
+StructID=      0
+Comment=     M 
+
+Number= 21
+Mixture= 0.005734
+B= 108.343185
+Alpha= 0.0067512 0.00239062 0.0140378 0.0043452 0.00365788 0.00689345 0.0148828 0.00715373 0.00789036 0.00614036 0.00289697 0.858995 0.00399721 0.00770961 0.00570515 0.0238176 0.011602 0.00591549 0.00167893 0.00353897 
+FullUpdate= 1
+QUpdate= 1
+StructID=      0
+Comment=     N 
+
+Number= 22
+Mixture= 0.022818
+B= 15.153304
+Alpha= 0.0417987 0.00360232 0.0113792 0.0152366 0.00564775 0.0123795 0.00606957 0.0091353 0.0165122 0.0167265 0.00490487 0.00915437 0.755604 0.0131375 0.012587 0.0283392 0.0189623 0.0140029 0.0012848 0.00353553 
+FullUpdate= 1
+QUpdate= 1
+StructID=      0
+Comment=     P 
+
+Number= 23
+Mixture= 0.005931
+B= 79.417511
+Alpha= 0.0142993 0.00266984 0.0053289 0.0321605 0.0028715 0.00426743 0.0257509 0.00565307 0.0106106 0.0161186 0.00955753 0.0104696 0.00638107 0.807311 0.0149106 0.0111968 0.00889459 0.00681482 0.00206658 0.00266624 
+FullUpdate= 1
+QUpdate= 1
+StructID=      0
+Comment=     Q 
+
+Number= 24
+Mixture= 0.011491
+B= 93.103897
+Alpha= 0.00756896 0.00314197 0.00296652 0.00327634 0.00194604 0.00467894 0.00721049 0.00406061 0.0277257 0.00663852 0.00217868 0.00577047 0.00473306 0.00953551 0.889701 0.00650859 0.00506022 0.00294281 0.00205549 0.00230062 
+FullUpdate= 1
+QUpdate= 1
+StructID=      0
+Comment=      R 
+
+Number= 25
+Mixture= 0.008219
+B= 47.504795
+Alpha= 0.0284818 0.00697155 0.00749796 0.00604665 0.00515171 0.00954817 0.00380684 0.00637929 0.0104463 0.00908885 0.00471437 0.0194592 0.00711823 0.00611827 0.00979722 0.707416 0.139256 0.00656298 0.0015377 0.00460086 
+FullUpdate= 1
+QUpdate= 1
+StructID=    0
+Comment=     S 
+
+Number= 26
+Mixture= 0.019050
+B= 14.027470
+Alpha= 0.0247201 0.00718027 0.00845584 0.0076239 0.00600101 0.0073401 0.00492149 0.0173757 0.0129878 0.0125773 0.0100452 0.0230424 0.00659406 0.0110314 0.0112037 0.107763 0.690341 0.0249364 0.00193884 0.00392074 
+FullUpdate= 1
+QUpdate= 1
+StructID=      0
+Comment=     T 
+
+Number= 27
+Mixture= 0.007047
+B= 76.958153
+Alpha= 0.0447488 0.00734525 0.00576457 0.00805666 0.00714188 0.00593389 0.0041663 0.0688592 0.00714299 0.0255115 0.00800708 0.00501678 0.00632646 0.00492002 0.00812967 0.0100074 0.0240134 0.745035 0.00126243 0.00261056 
+FullUpdate= 1
+QUpdate= 1
+StructID=      0
+Comment=     V 
+
+Number= 28
+Mixture= 0.003957
+B= 150.973328
+Alpha= 0.00517343 0.00213336 0.00350645 0.00390297 0.018439 0.0041919 0.0023655 0.00404231 0.00420998 0.0171406 0.00379068 0.00363696 0.00245861 0.00387467 0.00502035 0.00465674 0.00417283 0.00620977 0.888513 0.012561 
+FullUpdate= 1
+QUpdate= 1
+StructID=      0
+Comment=     W 
+
+Number= 29
+Mixture= 0.004904
+B= 30.653225
+Alpha= 0.0342049 0.00809912 0.0126852 0.0174701 0.156033 0.0118268 0.0431342 0.0204751 0.0164439 0.0363664 0.0129811 0.0131986 0.0103037 0.0116235 0.0159032 0.0287792 0.0176143 0.024986 0.0131845 0.494687 
+FullUpdate= 1
+QUpdate= 1
+StructID=      0
+Comment=     Y 
+
+/* $Header$ */
+/* $Header$ */
+/* $Header$ */
--- a/tool_dependencies.xml	Thu Jul 07 09:55:00 2016 -0400
+++ b/tool_dependencies.xml	Sun Jul 10 09:02:14 2016 -0400
@@ -1,9 +1,9 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="imagemagick" version="6.9.3">
-        <repository changeset_revision="942ae5bafee3" name="package_imagemagick_6_9_3" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <package name="graphicsmagick" version="1.3.20">
+        <repository changeset_revision="f2855f4cbc8f" name="package_graphicsmagick_1_3_20" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
-    <package name="meme" version="4.11.0">
-        <repository changeset_revision="5774a0e96d6f" name="package_meme_4_11_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <package name="meme" version="4.11.1">
+        <repository changeset_revision="336b41a99b8f" name="package_meme_4_11_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>