# HG changeset patch
# User dcorreia
# Date 1486390011 18000
# Node ID de8bd4852eaac7fa03fb533c10e0a22b02075164
# Parent  d336126a545fe43d7e422c8e941eaef640bd9982
planemo upload commit e0ca504b3313992020acf8ab7aed0a261237766e-dirty

diff -r d336126a545f -r de8bd4852eaa muscle.xml
--- a/muscle.xml	Thu Jan 26 09:53:10 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,120 +0,0 @@
-<tool id="muscle" name="MUSCLE" version="3.8.31.1">
-    <description>MUltiple Sequence Comparison by Log- Expectation</description>
-    <edam_operations>
-        <edam_operation>operation_0492</edam_operation>
-    </edam_operations>
-    <requirements>
-        <requirement type="package" version="3.8.31">muscle</requirement>
-    </requirements>
-    <version_command>
-      <![CDATA[  muscle -version ]]>
-    </version_command>
-    <command>
-                muscle
-                ##Do not display progress messages
-                -quiet
-                -in $input 
-                -out $output 
-                    
-                #if $mode.run == "custom" :
-                    -maxiters $mode.iterations
-                #else:
-                    -maxiters $mode.run
-                #end if
-                
-                -cluster1 $cluster
-                $diags
-                $outputFormat      
-    </command>
-    <inputs>
-        <param name="input" type="data" format="fasta" label="Source file" help="Fasta sequence file"/>
-        <conditional name="mode">
-            <param name="run" type="select" label="Run mode">
-                <option value="2">Progressive mode (faster)</option>
-                <option value="1">Fastest mode</option>
-                <option value="16" selected="true" >Full mode</option> 
-                <option value="custom">Custom mode</option>
-            </param>
-            <when value="2" />
-            <when value="1" />
-            <when value="16" />
-            <when value="custom">
-                <param name="iterations" type="integer" min='1' value="16" label="Maximum number of iterations" help="Increase the quality, increase the computing time"/>
-            </when>
-        </conditional>
-        
-        <param name="diags" type="boolean" truevalue="-diags" falsevalue="" checked="False" label="Find diagonals" help="Faster for similar sequences" />
-        
-        <param name="cluster" type="select" label="Clustering method">
-            <option value="upgma">UPGMA</option>
-            <option value="upgmb" selected="true" >UPGMB</option> 
-            <option value="neighborjoining">Neighbor Joining</option>
-        </param>
-        <param name="outputFormat" type="select" label="Output format" help="Either Fasta, Phylip">
-            <option value="" selected="true">Fasta</option>
-            <option value="-phyi">Phylip Interleaved format</option>
-            <option value="-phys">Phylip Sequential format</option>
-        </param>
-    </inputs>
-    <outputs>
-        <data name="output" format="fasta" label="MUSCLE Aligned sequencies ">
-            <change_format>
-                <when input="outputFormat" value="" format="fasta"/>
-                <when input="outputFormat" value="-phyi" format="phylip"/>
-                <when input="outputFormat" value="-phys" format="phylip"/>
-            </change_format>
-        </data>
-    </outputs>
-    <tests>
-        <test>
-            <param name="input" value="seqtest.fasta"/>
-            <param name="output" value="seqtest_aln.fasta"/>
-        </test>
-    </tests>
-    <help>
-
-.. class:: infomark
-
-**MUSCLE version 3.8.31, 2004**
-   
------
-   
-==============
- Please cite: 
-==============
-    
-"MUSCLE: multiple sequence_ alignment with high accuracy and high throughput."
-
-
-.. _sequence: http://nar.oxfordjournals.org/content/32/5/1792.long
-
-**Edgar R.C.**
-
-Nucleic Acids Res. 32(5):1792-1797, doi:10.1093/nar/gkh340, 2004.
-
-"MUSCLE: a multiple sequence alignment_ method with reduced time and space complexity."
-
-
-.. _alignment: http://www.biomedcentral.com/1471-2105/5/113/
-
-**Edgar R.C.**
-
-BMC Bioinformatics, (5) 113, 2004.
-
------    
-    
-==========
- Overview
-==========    
-
-MUSCLE is a program for creating multiple alignments of amino acid or nucleotide sequences. A range of options is provided that give you the choice of optimizing accuracy, speed, or some compromise between the two.
-
------
-
-For further informations, please visite the MUSCLE_ website.
-
-.. _MUSCLE: http://www.drive5.com/muscle/
-	
-    </help>
-
-</tool>
diff -r d336126a545f -r de8bd4852eaa muscle/muscle.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/muscle/muscle.xml	Mon Feb 06 09:06:51 2017 -0500
@@ -0,0 +1,120 @@
+<tool id="muscle" name="MUSCLE" version="3.8.31.1">
+    <description>MUltiple Sequence Comparison by Log- Expectation</description>
+    <edam_operations>
+        <edam_operation>operation_0492</edam_operation>
+    </edam_operations>
+    <requirements>
+        <requirement type="package" version="3.8.31">muscle</requirement>
+    </requirements>
+    <version_command>
+      <![CDATA[  muscle -version ]]>
+    </version_command>
+    <command>
+                muscle
+                ##Do not display progress messages
+                -quiet
+                -in $input 
+                -out $output 
+                    
+                #if $mode.run == "custom" :
+                    -maxiters $mode.iterations
+                #else:
+                    -maxiters $mode.run
+                #end if
+                
+                -cluster1 $cluster
+                $diags
+                $outputFormat      
+    </command>
+    <inputs>
+        <param name="input" type="data" format="fasta" label="Source file" help="Fasta sequence file"/>
+        <conditional name="mode">
+            <param name="run" type="select" label="Run mode">
+                <option value="2">Progressive mode (faster)</option>
+                <option value="1">Fastest mode</option>
+                <option value="16" selected="true" >Full mode</option> 
+                <option value="custom">Custom mode</option>
+            </param>
+            <when value="2" />
+            <when value="1" />
+            <when value="16" />
+            <when value="custom">
+                <param name="iterations" type="integer" min='1' value="16" label="Maximum number of iterations" help="Increase the quality, increase the computing time"/>
+            </when>
+        </conditional>
+        
+        <param name="diags" type="boolean" truevalue="-diags" falsevalue="" checked="False" label="Find diagonals" help="Faster for similar sequences" />
+        
+        <param name="cluster" type="select" label="Clustering method">
+            <option value="upgma">UPGMA</option>
+            <option value="upgmb" selected="true" >UPGMB</option> 
+            <option value="neighborjoining">Neighbor Joining</option>
+        </param>
+        <param name="outputFormat" type="select" label="Output format" help="Either Fasta, Phylip">
+            <option value="" selected="true">Fasta</option>
+            <option value="-phyi">Phylip Interleaved format</option>
+            <option value="-phys">Phylip Sequential format</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output" format="fasta" label="MUSCLE Aligned sequencies ">
+            <change_format>
+                <when input="outputFormat" value="" format="fasta"/>
+                <when input="outputFormat" value="-phyi" format="phylip"/>
+                <when input="outputFormat" value="-phys" format="phylip"/>
+            </change_format>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="seqtest.fasta"/>
+            <param name="output" value="seqtest_aln.fasta"/>
+        </test>
+    </tests>
+    <help>
+
+.. class:: infomark
+
+**MUSCLE version 3.8.31, 2004**
+   
+-----
+   
+==============
+ Please cite: 
+==============
+    
+"MUSCLE: multiple sequence_ alignment with high accuracy and high throughput."
+
+
+.. _sequence: http://nar.oxfordjournals.org/content/32/5/1792.long
+
+**Edgar R.C.**
+
+Nucleic Acids Res. 32(5):1792-1797, doi:10.1093/nar/gkh340, 2004.
+
+"MUSCLE: a multiple sequence alignment_ method with reduced time and space complexity."
+
+
+.. _alignment: http://www.biomedcentral.com/1471-2105/5/113/
+
+**Edgar R.C.**
+
+BMC Bioinformatics, (5) 113, 2004.
+
+-----    
+    
+==========
+ Overview
+==========    
+
+MUSCLE is a program for creating multiple alignments of amino acid or nucleotide sequences. A range of options is provided that give you the choice of optimizing accuracy, speed, or some compromise between the two.
+
+-----
+
+For further informations, please visite the MUSCLE_ website.
+
+.. _MUSCLE: http://www.drive5.com/muscle/
+	
+    </help>
+
+</tool>
diff -r d336126a545f -r de8bd4852eaa muscle/test-data/seqtest.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/muscle/test-data/seqtest.fasta	Mon Feb 06 09:06:51 2017 -0500
@@ -0,0 +1,35 @@
+>TestSequence1
+ERNECFLKHKDDDPNLPPVVKPEPEALCTAFQENNNKFLENYLYEVARRHPYFYGPELLY
+YVKQYKAILTECCQAACCQAADKATCLAPKAKVLKEKLLASSAKQRHKCASIQKFGERAA
+AFKAWSIARLSQRFPKADFMDLSKLVTDLSKIHKECCHGDLLECADDREDLAKYVQDVCA
+SFSSKLKECCDKPLLEKSHCISELENDDLPNDLPSITTDFVEDKDVCKLLNYKEAKDVFL
+GTFLYEYSRRHPEYAVSLLLRIAKGYEATLERCCATDDAHACYSKVFDELQPLVDEPQLL
+KLMKRNCELFENLGAYGFQNALIIRYTKKMPQVSTPTLLVISKELANMGNKCCTLPESKR
+>TestSequence2
+ERADCFASHRDDNPGFPLMVRPPVDELCASYQADAQMFAGKYLYEVARRYPYFYAPELLY
+YAQKLLYKDALAECCSAADKAACLTPKIDDLKESVMTSGAKQRFKCAGIEKFGERHGDLC
+AFKAWAVARLSQKFPNADFAEISKIVTDLTKINKECCHGDLLECADDRVELGKYMCDNKD
+SISSKLGKCCEKPLLEKGHCIAELERDDMPADLSPIEADFVEDKEVCKNYAEAKDVFLVC
+GTFLYELSRRHPEYSVVMLLRLAKGYEAVLEKCCATGDPPACYAKVFDELKPLIDEPDEL
+NLVKHNCELYGNLQEYGFQNALLIRYTKKMPQPTLVEVSRNLGKVGTKCCSLAEGERVCA
+>TestSequence3
+ERNECFLSHKDDSPDLPKLKPDPNTLCDEFKADEKKFWGKYLYEIARRHPYFYAPELLYA
+YANKYNGVFQECCQAEDKGACLLPKIETMREKVLTSSARQRLRCASIQKFGERHGDLVCA
+ALKAWSVARLSQKFPKAEFVEVTKLVTDLTKVHKECCHGDLLECADDRADLAKYICDNQD
+TISSKLKECCDKPLLEKSHCIAEVEKDAVPENLPPLTADFAEDKDVCKNYQEAKDAFLVC
+GSFLYEYSRRHPEYVLLRLALLKEYEATLEECCAKDDPHACYSTVFDKLKHLVDEPQVFL
+NLIKQNCDQFEKLGEYGFQNALIVRYTRKVPQVSTPTLVEVSRSLGKVGTRCCTKPESER
+>TestSequence4
+ERNECFLQHKDDNPNLPRLVRPEVDVMCTAFHDNEETFLKKYLYEIARRHPYFYAPELLF
+FAKRYKAAFTECCQAADKAACLLPKLDELRDEGKASSAKQRLKCASLQKFGERHGDLVCA
+AFKAWAVARLSQRFPKAEFAEVSKLVTDLTKVHTECCHGDLLECADDRADLAKYICENQD
+SISSKLKECCEKPLLEKSHCIAEVENDEMPADLPSLAADFVESKDVCKNYAEAKDVFLVC
+GMFLYEYARRHPRESVVLLLRLAKTYETTLEKCCAAADPHECYAKVFDEFKPLVEEPQLL
+NLIKQNCELFEQLGEYKFQNALLVRYTKKVPQVSTPTLVEVSRNLGKVGSKCCKHPEAKR
+>TestSequence5
+ERNECFLQHKDDNPGFGQLVTPEADAMCTAFHENEQRFLGKYLYEIARRHPYFYAPELLY
+YAEEYKGVFTECCEAADKAACLTPKVDALREKVLASSAKERLKCASLQKFGERHGDLVFL
+AFKAWSVARLSQKFPKAEFAEISKLVTDLAKIHKECCHGDLLECADDRADLAKYICENQD
+SISTKLKECCGKPVLEKSHCISEVERDELPADLPPLAVDFVEDKEVCKNYQEAKDVFLVC
+GTFLYEYSRRHPSSVSLLLRLAKEYEATLEKCCATDDPPACYAHVFDEFKPLVEEPHNQD
+NLVKTNCELFEKLGEYGFQNALLVRYTKKVPQVSTPTLVEVSRSLGKVGSKCCTHPEAER
\ No newline at end of file
diff -r d336126a545f -r de8bd4852eaa muscle/test-data/seqtest_aln.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/muscle/test-data/seqtest_aln.fasta	Mon Feb 06 09:06:51 2017 -0500
@@ -0,0 +1,40 @@
+>TestSequence1
+ERNECFLKHKDDDPNLPPVVKPEPEALCTAFQENNNKFLENYLYEVARRHPYFYGPELLY
+-YVKQ--YKAILTECCQAACCQAADKATCLAPKAKVLKEKLLASSAKQRHKCASIQKFGE
+RAA-----AFKAWSIARLSQRFPKADFMDLSKLVTDLSKIHKECCHGDLLECADDREDLA
+KYVQDVCASFSSKLKECCDKPLLEKSHCISELENDDLPNDLPSITTDFVEDKDVCKLLNY
+KEAKDVFL--GTFLYEYSRRHPEYAVSLLLRIAKGYEATLERCCATDDAHACYSKVFDEL
+QPLVDEPQLL-KLMKRNCELFENLGAYGFQNALIIRYTKKMPQVSTPTLLVISKELANMG
+NKCCTLPESKR---
+>TestSequence2
+ERADCFASHRDDNPGFPLMVRPPVDELCASYQADAQMFAGKYLYEVARRYPYFYAPELLY
+-YAQKLLYKDALAEC-----CSAADKAACLTPKIDDLKESVMTSGAKQRFKCAGIEKFGE
+RHGDLC--AFKAWAVARLSQKFPNADFAEISKIVTDLTKINKECCHGDLLECADDRVELG
+KYMCDNKDSISSKLGKCCEKPLLEKGHCIAELERDDMPADLSPIEADFVEDKEVCK--NY
+AEAKDVFLVCGTFLYELSRRHPEYSVVMLLRLAKGYEAVLEKCCATGDPPACYAKVFDEL
+KPLIDEPDEL-NLVKHNCELYGNLQEYGFQNALLIRYTKKMPQ---PTLVEVSRNLGKVG
+TKCCSLAEGERVCA
+>TestSequence3
+ERNECFLSHKDDSPDLPKL-KPDPNTLCDEFKADEKKFWGKYLYEIARRHPYFYAPELLY
+AYANK--YNGVFQEC-----CQAEDKGACLLPKIETMREKVLTSSARQRLRCASIQKFGE
+RHGDLVCAALKAWSVARLSQKFPKAEFVEVTKLVTDLTKVHKECCHGDLLECADDRADLA
+KYICDNQDTISSKLKECCDKPLLEKSHCIAEVEKDAVPENLPPLTADFAEDKDVCK--NY
+QEAKDAFLVCGSFLYEYSRRHPEY-VLLRLALLKEYEATLEECCAKDDPHACYSTVFDKL
+KHLVDEPQVFLNLIKQNCDQFEKLGEYGFQNALIVRYTRKVPQVSTPTLVEVSRSLGKVG
+TRCCTKPESER---
+>TestSequence4
+ERNECFLQHKDDNPNLPRLVRPEVDVMCTAFHDNEETFLKKYLYEIARRHPYFYAPELLF
+-FAKR--YKAAFTEC-----CQAADKAACLLPKLDELRDEGKASSAKQRLKCASLQKFGE
+RHGDLVCAAFKAWAVARLSQRFPKAEFAEVSKLVTDLTKVHTECCHGDLLECADDRADLA
+KYICENQDSISSKLKECCEKPLLEKSHCIAEVENDEMPADLPSLAADFVESKDVCK--NY
+AEAKDVFLVCGMFLYEYARRHPRESVVLLLRLAKTYETTLEKCCAAADPHECYAKVFDEF
+KPLVEEPQLL-NLIKQNCELFEQLGEYKFQNALLVRYTKKVPQVSTPTLVEVSRNLGKVG
+SKCCKHPEAKR---
+>TestSequence5
+ERNECFLQHKDDNPGFGQLVTPEADAMCTAFHENEQRFLGKYLYEIARRHPYFYAPELLY
+-YAEE--YKGVFTEC-----CEAADKAACLTPKVDALREKVLASSAKERLKCASLQKFGE
+RHGDLVFLAFKAWSVARLSQKFPKAEFAEISKLVTDLAKIHKECCHGDLLECADDRADLA
+KYICENQDSISTKLKECCGKPVLEKSHCISEVERDELPADLPPLAVDFVEDKEVCK--NY
+QEAKDVFLVCGTFLYEYSRRHPS-SVSLLLRLAKEYEATLEKCCATDDPPACYAHVFDEF
+KPLVEEPHNQDNLVKTNCELFEKLGEYGFQNALLVRYTKKVPQVSTPTLVEVSRSLGKVG
+SKCCTHPEAER---
diff -r d336126a545f -r de8bd4852eaa muscle/tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/muscle/tool_dependencies.xml	Mon Feb 06 09:06:51 2017 -0500
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+	<package name="muscle" version="3.8.31">
+		<repository changeset_revision="17c53de3f872" name="package_muscle_3_8_31" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+	</package>
+</tool_dependency>
diff -r d336126a545f -r de8bd4852eaa test-data/._seqtest_aln.fasta
Binary file test-data/._seqtest_aln.fasta has changed
diff -r d336126a545f -r de8bd4852eaa test-data/seqtest.fasta
--- a/test-data/seqtest.fasta	Thu Jan 26 09:53:10 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,35 +0,0 @@
->TestSequence1
-ERNECFLKHKDDDPNLPPVVKPEPEALCTAFQENNNKFLENYLYEVARRHPYFYGPELLY
-YVKQYKAILTECCQAACCQAADKATCLAPKAKVLKEKLLASSAKQRHKCASIQKFGERAA
-AFKAWSIARLSQRFPKADFMDLSKLVTDLSKIHKECCHGDLLECADDREDLAKYVQDVCA
-SFSSKLKECCDKPLLEKSHCISELENDDLPNDLPSITTDFVEDKDVCKLLNYKEAKDVFL
-GTFLYEYSRRHPEYAVSLLLRIAKGYEATLERCCATDDAHACYSKVFDELQPLVDEPQLL
-KLMKRNCELFENLGAYGFQNALIIRYTKKMPQVSTPTLLVISKELANMGNKCCTLPESKR
->TestSequence2
-ERADCFASHRDDNPGFPLMVRPPVDELCASYQADAQMFAGKYLYEVARRYPYFYAPELLY
-YAQKLLYKDALAECCSAADKAACLTPKIDDLKESVMTSGAKQRFKCAGIEKFGERHGDLC
-AFKAWAVARLSQKFPNADFAEISKIVTDLTKINKECCHGDLLECADDRVELGKYMCDNKD
-SISSKLGKCCEKPLLEKGHCIAELERDDMPADLSPIEADFVEDKEVCKNYAEAKDVFLVC
-GTFLYELSRRHPEYSVVMLLRLAKGYEAVLEKCCATGDPPACYAKVFDELKPLIDEPDEL
-NLVKHNCELYGNLQEYGFQNALLIRYTKKMPQPTLVEVSRNLGKVGTKCCSLAEGERVCA
->TestSequence3
-ERNECFLSHKDDSPDLPKLKPDPNTLCDEFKADEKKFWGKYLYEIARRHPYFYAPELLYA
-YANKYNGVFQECCQAEDKGACLLPKIETMREKVLTSSARQRLRCASIQKFGERHGDLVCA
-ALKAWSVARLSQKFPKAEFVEVTKLVTDLTKVHKECCHGDLLECADDRADLAKYICDNQD
-TISSKLKECCDKPLLEKSHCIAEVEKDAVPENLPPLTADFAEDKDVCKNYQEAKDAFLVC
-GSFLYEYSRRHPEYVLLRLALLKEYEATLEECCAKDDPHACYSTVFDKLKHLVDEPQVFL
-NLIKQNCDQFEKLGEYGFQNALIVRYTRKVPQVSTPTLVEVSRSLGKVGTRCCTKPESER
->TestSequence4
-ERNECFLQHKDDNPNLPRLVRPEVDVMCTAFHDNEETFLKKYLYEIARRHPYFYAPELLF
-FAKRYKAAFTECCQAADKAACLLPKLDELRDEGKASSAKQRLKCASLQKFGERHGDLVCA
-AFKAWAVARLSQRFPKAEFAEVSKLVTDLTKVHTECCHGDLLECADDRADLAKYICENQD
-SISSKLKECCEKPLLEKSHCIAEVENDEMPADLPSLAADFVESKDVCKNYAEAKDVFLVC
-GMFLYEYARRHPRESVVLLLRLAKTYETTLEKCCAAADPHECYAKVFDEFKPLVEEPQLL
-NLIKQNCELFEQLGEYKFQNALLVRYTKKVPQVSTPTLVEVSRNLGKVGSKCCKHPEAKR
->TestSequence5
-ERNECFLQHKDDNPGFGQLVTPEADAMCTAFHENEQRFLGKYLYEIARRHPYFYAPELLY
-YAEEYKGVFTECCEAADKAACLTPKVDALREKVLASSAKERLKCASLQKFGERHGDLVFL
-AFKAWSVARLSQKFPKAEFAEISKLVTDLAKIHKECCHGDLLECADDRADLAKYICENQD
-SISTKLKECCGKPVLEKSHCISEVERDELPADLPPLAVDFVEDKEVCKNYQEAKDVFLVC
-GTFLYEYSRRHPSSVSLLLRLAKEYEATLEKCCATDDPPACYAHVFDEFKPLVEEPHNQD
-NLVKTNCELFEKLGEYGFQNALLVRYTKKVPQVSTPTLVEVSRSLGKVGSKCCTHPEAER
\ No newline at end of file
diff -r d336126a545f -r de8bd4852eaa test-data/seqtest_aln.fasta
--- a/test-data/seqtest_aln.fasta	Thu Jan 26 09:53:10 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,40 +0,0 @@
->TestSequence1
-ERNECFLKHKDDDPNLPPVVKPEPEALCTAFQENNNKFLENYLYEVARRHPYFYGPELLY
--YVKQ--YKAILTECCQAACCQAADKATCLAPKAKVLKEKLLASSAKQRHKCASIQKFGE
-RAA-----AFKAWSIARLSQRFPKADFMDLSKLVTDLSKIHKECCHGDLLECADDREDLA
-KYVQDVCASFSSKLKECCDKPLLEKSHCISELENDDLPNDLPSITTDFVEDKDVCKLLNY
-KEAKDVFL--GTFLYEYSRRHPEYAVSLLLRIAKGYEATLERCCATDDAHACYSKVFDEL
-QPLVDEPQLL-KLMKRNCELFENLGAYGFQNALIIRYTKKMPQVSTPTLLVISKELANMG
-NKCCTLPESKR---
->TestSequence2
-ERADCFASHRDDNPGFPLMVRPPVDELCASYQADAQMFAGKYLYEVARRYPYFYAPELLY
--YAQKLLYKDALAEC-----CSAADKAACLTPKIDDLKESVMTSGAKQRFKCAGIEKFGE
-RHGDLC--AFKAWAVARLSQKFPNADFAEISKIVTDLTKINKECCHGDLLECADDRVELG
-KYMCDNKDSISSKLGKCCEKPLLEKGHCIAELERDDMPADLSPIEADFVEDKEVCK--NY
-AEAKDVFLVCGTFLYELSRRHPEYSVVMLLRLAKGYEAVLEKCCATGDPPACYAKVFDEL
-KPLIDEPDEL-NLVKHNCELYGNLQEYGFQNALLIRYTKKMPQ---PTLVEVSRNLGKVG
-TKCCSLAEGERVCA
->TestSequence3
-ERNECFLSHKDDSPDLPKL-KPDPNTLCDEFKADEKKFWGKYLYEIARRHPYFYAPELLY
-AYANK--YNGVFQEC-----CQAEDKGACLLPKIETMREKVLTSSARQRLRCASIQKFGE
-RHGDLVCAALKAWSVARLSQKFPKAEFVEVTKLVTDLTKVHKECCHGDLLECADDRADLA
-KYICDNQDTISSKLKECCDKPLLEKSHCIAEVEKDAVPENLPPLTADFAEDKDVCK--NY
-QEAKDAFLVCGSFLYEYSRRHPEY-VLLRLALLKEYEATLEECCAKDDPHACYSTVFDKL
-KHLVDEPQVFLNLIKQNCDQFEKLGEYGFQNALIVRYTRKVPQVSTPTLVEVSRSLGKVG
-TRCCTKPESER---
->TestSequence4
-ERNECFLQHKDDNPNLPRLVRPEVDVMCTAFHDNEETFLKKYLYEIARRHPYFYAPELLF
--FAKR--YKAAFTEC-----CQAADKAACLLPKLDELRDEGKASSAKQRLKCASLQKFGE
-RHGDLVCAAFKAWAVARLSQRFPKAEFAEVSKLVTDLTKVHTECCHGDLLECADDRADLA
-KYICENQDSISSKLKECCEKPLLEKSHCIAEVENDEMPADLPSLAADFVESKDVCK--NY
-AEAKDVFLVCGMFLYEYARRHPRESVVLLLRLAKTYETTLEKCCAAADPHECYAKVFDEF
-KPLVEEPQLL-NLIKQNCELFEQLGEYKFQNALLVRYTKKVPQVSTPTLVEVSRNLGKVG
-SKCCKHPEAKR---
->TestSequence5
-ERNECFLQHKDDNPGFGQLVTPEADAMCTAFHENEQRFLGKYLYEIARRHPYFYAPELLY
--YAEE--YKGVFTEC-----CEAADKAACLTPKVDALREKVLASSAKERLKCASLQKFGE
-RHGDLVFLAFKAWSVARLSQKFPKAEFAEISKLVTDLAKIHKECCHGDLLECADDRADLA
-KYICENQDSISTKLKECCGKPVLEKSHCISEVERDELPADLPPLAVDFVEDKEVCK--NY
-QEAKDVFLVCGTFLYEYSRRHPS-SVSLLLRLAKEYEATLEKCCATDDPPACYAHVFDEF
-KPLVEEPHNQDNLVKTNCELFEKLGEYGFQNALLVRYTKKVPQVSTPTLVEVSRSLGKVG
-SKCCTHPEAER---
diff -r d336126a545f -r de8bd4852eaa tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Jan 26 09:53:10 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-	<package name="muscle" version="3.8.31">
-		<repository changeset_revision="17c53de3f872" name="package_muscle_3_8_31" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-	</package>
-</tool_dependency>