Mercurial > repos > yating-l > gbtofasta

changeset 4:3568235c44bf draft

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planemo upload commit 4737b5365c135058ff6dc65a3d9f249b11f1751a-dirty
author yating-l
date Tue, 08 Aug 2017 17:53:39 -0400
parents 894d96efad6d
children e195691d3e71
files gbToFasta.xml test-data/Gallus_gallus_RefSeq.ix tool_dependencies.xml
diffstat 3 files changed, 325 insertions(+), 23 deletions(-) [+]
line wrap: on
line diff
--- a/gbToFasta.xml	Mon Jun 05 12:00:08 2017 -0400
+++ b/gbToFasta.xml	Tue Aug 08 17:53:39 2017 -0400
@@ -11,6 +11,17 @@
             outputra
             outputta
             '${gbfile}'
+    &&
+    raToTab
+            -cols=acc,def
+            outputra
+            outputinfo
+    &&
+    ixIxx
+            outputinfo
+            ${index_ix}
+            index_ixx
+            
       #if $cds == "yes"
             && raToTab
                   -cols=acc,cds
@@ -29,6 +40,7 @@
       </inputs>
       <outputs>
             <data format="fasta" name="outputfa" label="${tool.name} on ${on_string}:fasta"></data>
+            <data format="txt" name="index_ix" label="${tool.name} on ${on_string}:txt"></data>
             <data format="tabular" name="outputcds" label="${tool.name} on ${on_string}:cds">
                   <filter>cds == "yes"</filter>
             </data>
@@ -39,11 +51,13 @@
             <param name="cds" value="yes" />
             <output name="outputfa" value="Gallus_gallus_RefSeq.fa" />
             <output name="outputcds" value="Gallus_gallus_RefSeq.cds" />
+            <output name="index_ix" value="Gallus_gallus_RefSeq.ix" />
       </test>
       <test>
             <param name="gbfile" value="Gallus_gallus_RefSeq.gb" />
             <param name="cds" value="no" />
             <output name="outputfa" value="Gallus_gallus_RefSeq.fa" />
+            <output name="index_ix" value="Gallus_gallus_RefSeq.ix" />
       </test>
   </tests> 
   <help>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Gallus_gallus_RefSeq.ix	Tue Aug 08 17:53:39 2017 -0400
@@ -0,0 +1,309 @@
+1 NM_001001775,13 NM_001004378,8 NM_001031150,7 NM_001113708,10 NM_001128828,7 NM_001128828,11 NM_001167759,11 NM_001194996,11 NM_001195561,8 NM_001199429,4 NM_001199712,8 NM_001242604,7 NM_001257373,7 NM_001271936,6 NM_001277476,13 NM_001277630,11 NM_001277657,8 NM_001278100,11 NM_001278545,6 NM_001290554,8 NM_001305109,5 NM_001305109,9 NM_001305110,5 NM_001305111,5 NM_001305112,5 NM_001317736,8 NM_001328355,7 NM_001347710,9 NM_204172,7 NM_204471,10 NM_204727,5 NM_204843,7 NM_204992,9 NM_205501,5
+11 NM_001031536,7
+11-like NM_001347710,8
+12 NM_001030706,7
+12b NM_204727,8
+13 NM_001006577,7 NM_001194996,7
+136 NM_001317736,5
+15 NM_001199231,7 NM_204766,6
+179 NM_001277797,7
+1a NM_204182,6
+1b NM_001293103,5
+2 NM_001001775,9 NM_001006577,11 NM_001111014,9 NM_001111014,13 NM_001167758,11 NM_001199713,8 NM_001201399,9 NM_001242604,11 NM_001252284,7 NM_001271964,10 NM_001277476,9 NM_001277477,9 NM_001277477,13 NM_001277631,11 NM_001278102,11 NM_001305110,9 NM_001347710,6 NM_001347945,5 NM_001348012,10 NM_204212,4 NM_205038,4
+20 NM_001145430,7
+26s NM_001030706,4
+3 NM_001005808,5 NM_001199613,5 NM_001271965,10 NM_001278104,11 NM_001305111,9 NM_001328354,6 NM_204650,5 NM_204996,5 NM_205054,4 NM_205405,5
+4 NM_001031013,11 NM_001195562,6 NM_001271966,10 NM_001290554,6 NM_001305112,9
+48 NM_001030974,7
+4a NM_001201399,5 NM_204992,5
+5 NM_001030697,6 NM_001257371,7
+6 NM_001277490,7
+7 NM_001006176,4 NM_001163651,9 NM_001281486,7 NM_001348012,6 NM_204471,6
+8 NM_001293169,5
+9 NM_001305089,5
+a NM_001030587,5 NM_001031013,8 NM_001277797,9 NM_205054,8
+a2 NM_001184757,4
+aamdc NM_001278100,8 NM_001278102,8 NM_001278104,8
+aarsd1 NM_001328355,8
+acetyltransferase NM_001277490,4
+acid NM_001277476,4 NM_001277477,4
+activated NM_001004378,5
+activating NM_204843,5
+adhesion NM_001128828,5 NM_001242604,5
+adipogenesis NM_001278100,3 NM_001278102,3 NM_001278104,3
+adipoq NM_001163651,5
+agr3 NM_001199613,11
+alanyl-trna NM_001328355,3
+alpha NM_001005808,7 NM_001012804,6 NM_001113708,6 NM_001271964,6 NM_001271965,6 NM_001271966,6
+aminomethyltransferase NM_204788,3
+ampa NM_001001775,6 NM_001111014,6
+amt NM_204788,4
+and NM_001163651,4 NM_001277841,7
+anterior NM_001199613,3
+argininosuccinate NM_205501,3
+asl1 NM_205501,6
+assembly NM_001006211,5 NM_001271936,5
+associated NM_001030587,8 NM_001195561,5 NM_001257373,5 NM_001278100,4 NM_001278102,4 NM_001278104,4
+atpase NM_001024456,8
+avbd3 NM_204650,6
+avian NM_204650,3
+beta NM_001201399,4 NM_001318995,8 NM_001318995,17 NM_204992,4
+beta-defensin NM_204650,4
+bglap NM_205387,6
+binding NM_001030974,4
+blb2 NM_001318995,10 NM_001318995,19
+blood NM_001290554,10
+bone NM_205387,3
+c NM_001004378,6 NM_001012804,5 NM_001277630,7 NM_001277631,7
+c2 NM_205450,4
+c3 NM_205405,6
+cacfd1 NM_001277657,9
+calca NM_001113708,7 NM_001271964,7 NM_001271965,7 NM_001271966,7
+calcitonin NM_001113708,3 NM_001271964,3 NM_001271965,3 NM_001271966,3
+calcium NM_001277657,3
+carrier NM_001290554,4 NM_001347710,4
+cell NM_001128828,4 NM_001242604,4
+chain NM_001318995,9 NM_001318995,18 NM_204766,5
+channel NM_001277657,4
+ckmt1a NM_204182,7
+class NM_001031013,7 NM_001318995,6 NM_001318995,14
+cluster NM_001006305,5 NM_001271936,4
+coat NM_001277841,9
+complement NM_205405,3
+complex NM_001006577,6 NM_001031172,5 NM_001031536,6 NM_001194996,6 NM_001277490,5 NM_001277841,10 NM_001292086,9 NM_001318995,5
+component NM_001277841,11 NM_001292086,10 NM_205405,4
+conjugating NM_001195424,4
+containing NM_001031013,10 NM_001195561,7 NM_001195562,5 NM_001277657,7 NM_001278100,7 NM_001278102,7 NM_001278104,7 NM_001328355,6
+copii NM_001277841,8
+coro7 NM_001006176,5
+coronin NM_001006176,3
+creatine NM_204182,3
+cytosolic NM_001328354,7
+d NM_001318995,16
+dctn2 NM_001347945,6
+decarboxylase NM_001305109,4 NM_001305110,4 NM_001305111,4 NM_001305112,4
+defb4a NM_001201399,6 NM_204992,6
+defensin NM_001201399,3 NM_204992,3
+dehydrogenase NM_001005808,4
+density NM_001031013,4
+development NM_204172,4
+diego NM_001290554,9
+dissociation NM_001031150,5
+disulphide NM_001199613,7
+dna NM_001167758,5 NM_001167759,5
+domain NM_001031013,9 NM_001195561,6 NM_001195562,4 NM_001277657,6 NM_001278100,6 NM_001278102,6 NM_001278104,6 NM_001328355,5
+dynactin NM_001347945,3
+e NM_001328354,4
+e2 NM_001195424,6
+e3 NM_001195424,7
+echdc1 NM_001305109,6 NM_001305110,6 NM_001305111,6 NM_001305112,6
+elongator NM_001277490,3
+elp6 NM_001277490,8
+enzyme NM_001195424,5
+ethylmalonyl-coa NM_001305109,3 NM_001305110,3 NM_001305111,3 NM_001305112,3
+exchange NM_001006211,8
+factor NM_001006211,9 NM_001024456,5 NM_001293169,9 NM_001305089,9
+fam179a NM_001277797,10
+family NM_001163651,7 NM_001199613,9 NM_001257371,5 NM_001277797,3 NM_001290554,5 NM_001317736,6 NM_001347710,5
+fast NM_205450,5
+flower NM_001277657,5
+for NM_001004378,4
+fusing NM_001024456,7
+gallus NM_001001775,1 NM_001001775,2 NM_001004378,1 NM_001004378,2 NM_001005808,1 NM_001005808,2 NM_001006176,1 NM_001006176,2 NM_001006211,1 NM_001006211,2 NM_001006305,1 NM_001006305,2 NM_001006355,1 NM_001006355,2 NM_001006577,1 NM_001006577,2 NM_001012804,1 NM_001012804,2 NM_001024456,1 NM_001024456,2 NM_001030587,1 NM_001030587,2 NM_001030697,1 NM_001030697,2 NM_001030706,1 NM_001030706,2 NM_001030974,1 NM_001030974,2 NM_001031013,1 NM_001031013,2 NM_001031150,1 NM_001031150,2 NM_001031172,1 NM_001031172,2 NM_001031536,1 NM_001031536,2 NM_001044640,1 NM_001044640,2 NM_001110060,1 NM_001110060,2 NM_001111014,1 NM_001111014,2 NM_001113708,1 NM_001113708,2 NM_001115017,1 NM_001115017,2 NM_001128828,1 NM_001128828,2 NM_001145430,1 NM_001145430,2 NM_001163651,1 NM_001163651,2 NM_001167726,1 NM_001167726,2 NM_001167758,1 NM_001167758,2 NM_001167759,1 NM_001167759,2 NM_001184757,1 NM_001184757,2 NM_001194996,1 NM_001194996,2 NM_001195424,1 NM_001195424,2 NM_001195561,1 NM_001195561,2 NM_001195562,1 NM_001195562,2 NM_001199231,1 NM_001199231,2 NM_001199429,1 NM_001199429,2 NM_001199613,1 NM_001199613,2 NM_001199712,1 NM_001199712,2 NM_001199713,1 NM_001199713,2 NM_001201399,1 NM_001201399,2 NM_001242604,1 NM_001242604,2 NM_001252284,1 NM_001252284,2 NM_001257371,1 NM_001257371,2 NM_001257373,1 NM_001257373,2 NM_001271894,1 NM_001271894,2 NM_001271936,1 NM_001271936,2 NM_001271964,1 NM_001271964,2 NM_001271965,1 NM_001271965,2 NM_001271966,1 NM_001271966,2 NM_001277476,1 NM_001277476,2 NM_001277477,1 NM_001277477,2 NM_001277490,1 NM_001277490,2 NM_001277630,1 NM_001277630,2 NM_001277631,1 NM_001277631,2 NM_001277657,1 NM_001277657,2 NM_001277715,1 NM_001277715,2 NM_001277797,1 NM_001277797,2 NM_001277841,1 NM_001277841,2 NM_001278100,1 NM_001278100,2 NM_001278102,1 NM_001278102,2 NM_001278104,1 NM_001278104,2 NM_001278545,1 NM_001278545,2 NM_001281486,1 NM_001281486,2 NM_001290554,1 NM_001290554,2 NM_001292086,1 NM_001292086,2 NM_001293103,1 NM_001293103,2 NM_001293169,1 NM_001293169,2 NM_001305089,1 NM_001305089,2 NM_001305109,1 NM_001305109,2 NM_001305110,1 NM_001305110,2 NM_001305111,1 NM_001305111,2 NM_001305112,1 NM_001305112,2 NM_001317736,1 NM_001317736,2 NM_001318432,1 NM_001318432,2 NM_001318982,1 NM_001318982,2 NM_001318995,1 NM_001318995,2 NM_001322804,1 NM_001322804,2 NM_001328354,1 NM_001328354,2 NM_001328355,1 NM_001328355,2 NM_001347710,1 NM_001347710,2 NM_001347945,1 NM_001347945,2 NM_001348012,1 NM_001348012,2 NM_204172,1 NM_204172,2 NM_204182,1 NM_204182,2 NM_204212,1 NM_204212,2 NM_204471,1 NM_204471,2 NM_204650,1 NM_204650,2 NM_204727,1 NM_204727,2 NM_204766,1 NM_204766,2 NM_204788,1 NM_204788,2 NM_204843,1 NM_204843,2 NM_204992,1 NM_204992,2 NM_204996,1 NM_204996,2 NM_205038,1 NM_205038,2 NM_205054,1 NM_205054,2 NM_205307,1 NM_205307,2 NM_205387,1 NM_205387,2 NM_205405,1 NM_205405,2 NM_205450,1 NM_205450,2 NM_205501,1 NM_205501,2
+gamma-carboxyglutamate NM_205387,4
+garp NM_001031172,4
+glutamate NM_001001775,3 NM_001111014,3
+gradient NM_001199613,4
+gria2 NM_001001775,10 NM_001111014,10
+group NM_001184757,5 NM_001290554,11 NM_205054,5
+gtpase NM_001257373,6 NM_204843,4
+gtpase-gdp NM_001031150,4
+guanine NM_001006211,6
+heavy NM_204766,4
+hexokinase NM_204212,3
+histamine NM_001318432,3
+histocompatibility NM_001318995,4
+hk2 NM_204212,5
+hla NM_001318995,13
+homolog NM_001030587,4 NM_001167758,4 NM_001167759,4 NM_001277715,4 NM_001277841,4 NM_001292086,4
+homologous NM_001293169,6 NM_001305089,6
+i NM_001277630,5 NM_001277631,5 NM_205054,6
+idh3a NM_001005808,8
+igll1 NM_001278545,7
+ii NM_001292086,8 NM_001318995,7 NM_001318995,15
+immunoglobulin NM_001278545,3
+imp4 NM_001277715,3 NM_001277715,9
+induced NM_001277476,8 NM_001277477,8
+integral NM_001145430,4 NM_001199231,4 NM_001281486,4
+ionotropic NM_001001775,4 NM_001111014,4
+iron-sulfur NM_001006305,4 NM_001271936,3
+isca1 NM_001271936,7
+isocitrate NM_001005808,3
+isomerase NM_001199613,8
+jak3 NM_204996,6
+janus NM_204996,3
+kinase NM_001004378,7 NM_001012804,4 NM_204182,4 NM_204996,4 NM_205307,7
+lambda-like NM_001278545,4
+ldlrad4 NM_001031013,12
+leo1 NM_001292086,3 NM_001292086,11
+like NM_001252284,6 NM_001271894,4 NM_001328354,8
+limb NM_204172,3
+lipoprotein NM_001031013,5
+lmbr1 NM_204172,8
+loc423300 NM_001199712,4 NM_001199713,4
+loc768735 NM_001318982,3 NM_001318982,4
+loc771456 NM_001318432,5
+low NM_001031013,3
+lyase NM_205501,4
+maintenance NM_001293169,4 NM_001305089,4
+major NM_001318995,3
+mcm8 NM_001293169,10
+mcm9 NM_001305089,10
+melatonin NM_001293103,3
+member NM_001163651,8 NM_001199613,10 NM_001257371,6 NM_001277797,8 NM_001290554,7 NM_001317736,7 NM_001347710,7
+membrane NM_001145430,5 NM_001199231,5 NM_001281486,5 NM_204172,5
+microsomal NM_001322804,3
+minichromosome NM_001293169,3 NM_001305089,3
+mitochondrial NM_001257373,3 NM_204182,5
+molecule NM_001128828,6 NM_001242604,6
+mon1 NM_001030587,3
+mon1a NM_001030587,9
+motif NM_001030974,5
+mpzl2 NM_001252284,8
+mrna NM_001001775,14 NM_001004378,10 NM_001005808,9 NM_001006176,6 NM_001006211,11 NM_001006305,8 NM_001006355,7 NM_001006577,12 NM_001012804,8 NM_001024456,10 NM_001030587,10 NM_001030697,8 NM_001030706,9 NM_001030974,9 NM_001031013,13 NM_001031150,9 NM_001031172,8 NM_001031536,9 NM_001044640,7 NM_001110060,7 NM_001111014,14 NM_001113708,11 NM_001115017,6 NM_001128828,12 NM_001145430,9 NM_001163651,11 NM_001167726,8 NM_001167758,12 NM_001167759,12 NM_001184757,8 NM_001194996,12 NM_001195424,9 NM_001195561,11 NM_001195562,8 NM_001199231,9 NM_001199429,6 NM_001199613,12 NM_001199712,9 NM_001199713,9 NM_001201399,10 NM_001242604,12 NM_001252284,9 NM_001257371,9 NM_001257373,9 NM_001271894,6 NM_001271936,8 NM_001271964,11 NM_001271965,11 NM_001271966,11 NM_001277476,14 NM_001277477,14 NM_001277490,9 NM_001277630,12 NM_001277631,12 NM_001277657,10 NM_001277715,10 NM_001277797,11 NM_001277841,13 NM_001278100,12 NM_001278102,12 NM_001278104,12 NM_001278545,8 NM_001281486,9 NM_001290554,13 NM_001292086,12 NM_001293103,7 NM_001293169,11 NM_001305089,11 NM_001305109,10 NM_001305110,10 NM_001305111,10 NM_001305112,10 NM_001317736,10 NM_001318432,6 NM_001318982,5 NM_001318995,20 NM_001322804,8 NM_001328354,10 NM_001328355,9 NM_001347710,11 NM_001347945,7 NM_001348012,11 NM_204172,9 NM_204182,8 NM_204212,6 NM_204471,11 NM_204650,7 NM_204727,10 NM_204766,8 NM_204788,5 NM_204843,9 NM_204992,10 NM_204996,7 NM_205038,6 NM_205054,10 NM_205307,9 NM_205387,7 NM_205405,7 NM_205450,9 NM_205501,7
+mtg1 NM_001257373,8
+mth938 NM_001278100,5 NM_001278102,5 NM_001278104,5
+mtnr1b NM_001293103,6
+mttpl NM_001322804,7
+myelin NM_001252284,3
+myh15 NM_204766,7
+myosin NM_204766,3
+n-ethylmaleimide NM_001024456,3
+n-methyltransferase-like NM_001318432,4
+nad NM_001005808,6
+ncam1 NM_001128828,8 NM_001242604,8
+nephrocystin NM_001199429,3
+neural NM_001128828,3 NM_001242604,3
+nf-kb NM_001167726,5
+nfu1 NM_001006305,3 NM_001006305,7
+nm23 NM_001257371,4
+nme NM_001257371,3
+nme5 NM_001257371,8
+non-atpase NM_001030706,6
+nova1 NM_001199712,5 NM_001199713,5
+nphp1 NM_001199429,5
+nsf NM_001024456,9
+nuclear NM_001277841,5
+nucleolar NM_001277715,7
+nucleotide NM_001006211,7
+o NM_001115017,4
+paf1 NM_001292086,5
+paqr7 NM_001163651,10
+particle NM_001006577,5 NM_001031536,5 NM_001194996,5
+patched NM_001195562,3
+pepsinogen NM_205054,3 NM_205054,7
+peptidase NM_001348012,5 NM_204471,5
+peripherin NM_205038,3
+pga3 NM_205054,9
+phosphatase NM_204727,4
+phosphoinositide-3-kinase NM_001030697,3
+phospholipase NM_001184757,3
+pik3r5 NM_001030697,7
+pla2g10 NM_001184757,7
+podocalyxin NM_001271894,3
+podxl NM_001271894,5
+polr1c NM_001277630,8 NM_001277631,8
+polymerase NM_001277630,4 NM_001277631,4 NM_001292086,7
+polypeptide NM_001113708,5 NM_001271964,5 NM_001271965,5 NM_001271966,5 NM_001278545,5
+pore NM_001277841,6
+ppp1r12b NM_204727,9
+prkca NM_001012804,7
+progestin NM_001163651,3
+prolyl-trna NM_001195561,3
+prorsd1p NM_001195561,10
+prostaglandin NM_001328354,3
+proteasome NM_001030706,3
+protein NM_001006355,4 NM_001006577,4 NM_001012804,3 NM_001030974,6 NM_001031536,4 NM_001044640,4 NM_001110060,4 NM_001145430,6 NM_001167758,7 NM_001167759,7 NM_001194996,4 NM_001199231,6 NM_001199613,6 NM_001252284,4 NM_001281486,6 NM_001317736,4 NM_204172,6 NM_204727,3 NM_204843,6 NM_205387,5
+protein-like NM_001322804,6
+proto-oncogene NM_001167726,4 NM_205307,4
+prph2 NM_205038,5
+pseudogene NM_001195561,9
+psmd12 NM_001030706,8
+ptchd4 NM_001195562,7
+ptges3l NM_001328354,9
+rab-18-b NM_001006355,5
+rab-23 NM_001110060,5
+rab-6a NM_001044640,5
+rab18 NM_001006355,6
+rab23 NM_001110060,6
+rab6a NM_001044640,6
+rack1 NM_001004378,9
+rad52 NM_001167758,3 NM_001167758,8 NM_001167759,3 NM_001167759,8
+raf-1 NM_205307,3
+raf1 NM_205307,8
+rap1 NM_001031150,3 NM_204843,3
+rap1gap1 NM_204843,8
+rap1gds1 NM_001031150,8
+rarres2 NM_001277476,10 NM_001277477,10
+ras-related NM_001006355,3 NM_001044640,3 NM_001110060,3
+rbm48 NM_001030974,8
+receptor NM_001001775,5 NM_001004378,3 NM_001031013,6 NM_001111014,5 NM_001163651,6 NM_001277476,5 NM_001277477,5 NM_001293103,4
+recombination NM_001293169,7 NM_001305089,7
+regulatory NM_001030697,4 NM_204727,6
+rel NM_001167726,3 NM_001167726,7
+related NM_001113708,4 NM_001271964,4 NM_001271965,4 NM_001271966,4
+repair NM_001167758,6 NM_001167759,6 NM_001293169,8 NM_001305089,8
+responder NM_001277476,6 NM_001277477,6
+retinoic NM_001277476,3 NM_001277477,3
+ribonucleoprotein NM_001277715,8
+ribosome NM_001006211,4 NM_001257373,4
+rna NM_001030974,3 NM_001277630,3 NM_001277631,3 NM_001292086,6
+sbds NM_001006211,3 NM_001006211,10
+scaffold NM_001006305,6
+sec13 NM_001277841,3 NM_001277841,12
+secretory NM_001030587,6
+selenoo NM_001115017,5
+selenoprotein NM_001115017,3
+sensitive NM_001024456,4
+sequence NM_001277797,5
+serine NM_205307,5
+similar NM_001318995,11
+similarity NM_001277797,6
+skeletal NM_205450,6
+slc2a11l1 NM_001347710,10
+slc4a1 NM_001290554,12
+small NM_001145430,3 NM_001199231,3 NM_001277715,6 NM_001281486,3
+smim15 NM_001199231,8
+smim20 NM_001145430,8
+smim7 NM_001281486,8
+solute NM_001290554,3 NM_001347710,3
+specific NM_001348012,4 NM_204471,4
+stimulator NM_001031150,6
+subunit NM_001001775,8 NM_001030697,5 NM_001030706,5 NM_001031172,6 NM_001111014,8 NM_001167726,6 NM_001277490,6 NM_001277630,6 NM_001277631,6 NM_001347945,4 NM_204727,7
+synthase NM_001328354,5
+synthetase NM_001195561,4 NM_001328355,4
+tazarotene NM_001277476,7 NM_001277477,7
+threonine NM_205307,6
+tmem136-1 NM_001317736,9
+tnnc2 NM_205450,8
+to NM_001318995,12
+trafficking NM_001006577,3 NM_001030587,7 NM_001031536,3 NM_001194996,3
+transcript NM_001001775,11 NM_001006577,9 NM_001111014,11 NM_001113708,8 NM_001128828,9 NM_001167758,9 NM_001167759,9 NM_001194996,9 NM_001199712,6 NM_001199713,6 NM_001201399,7 NM_001242604,9 NM_001271964,8 NM_001271965,8 NM_001271966,8 NM_001277476,11 NM_001277477,11 NM_001277630,9 NM_001277631,9 NM_001278100,9 NM_001278102,9 NM_001278104,9 NM_001305109,7 NM_001305110,7 NM_001305111,7 NM_001305112,7 NM_001348012,8 NM_204471,8 NM_204992,7
+transfer NM_001322804,5
+transmembrane NM_001317736,3
+trappc11 NM_001031536,8
+trappc13 NM_001006577,8 NM_001194996,8
+triglyceride NM_001322804,4
+troponin NM_205450,3
+type NM_001001775,7 NM_001111014,7 NM_205450,7
+u3 NM_001277715,5
+ube2e3 NM_001195424,8
+ubiquitin NM_001195424,3 NM_001348012,3 NM_204471,3
+uncharacterized NM_001199712,3 NM_001199713,3
+usp7 NM_001348012,7 NM_204471,7
+variant NM_001001775,12 NM_001006577,10 NM_001111014,12 NM_001113708,9 NM_001128828,10 NM_001167758,10 NM_001167759,10 NM_001194996,10 NM_001199712,7 NM_001199713,7 NM_001201399,8 NM_001242604,10 NM_001271964,9 NM_001271965,9 NM_001271966,9 NM_001277476,12 NM_001277477,12 NM_001277630,10 NM_001277631,10 NM_001278100,10 NM_001278102,10 NM_001278104,10 NM_001305109,8 NM_001305110,8 NM_001305111,8 NM_001305112,8 NM_001348012,9 NM_204471,9 NM_204992,8
+vesicle NM_001024456,6
+vps51 NM_001031172,3 NM_001031172,7
+with NM_001277797,4
+x NM_001184757,6
+zero NM_001252284,5
--- a/tool_dependencies.xml	Mon Jun 05 12:00:08 2017 -0400
+++ b/tool_dependencies.xml	Tue Aug 08 17:53:39 2017 -0400
@@ -1,27 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <!-- required tools:
-        - blat
-        - sort
-        - pslReps
-        - faPolyASizes
-        - pslCDnaFilter
-    -->
     <package name="ucsc_tools_340_for_BLAT" version="1.0">
-        <install version="1.0">
-            <actions_group>
-                <actions architecture="x86_64" os="linux">
-                    <action type="download_by_url">http://old-gep.wustl.edu/~galaxy/package_ucsc_tools_340_for_BLAT.tar.gz</action>
-                    <action type="move_directory_files">
-                        <source_directory>.</source_directory>
-                        <destination_directory>$INSTALL_DIR/bin</destination_directory>
-                    </action>
-                </actions>
-                <action type="set_environment">
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
-                </action>
-            </actions_group>
-        </install>
-        <readme>The tools and utilities were created by the UCSC Genome Bioinformatics Group</readme>
+        <repository changeset_revision="cb552dc29cb9" name="package_ucsc_blat_340" owner="yating-l" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
-</tool_dependency>
\ No newline at end of file
+</tool_dependency>