Mercurial > repos > pharaohs_son > tags_in_fasta

changeset 0:f07833b30bdd draft

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Uploaded
author pharaohs_son
date Fri, 19 Jun 2020 18:05:17 -0400
parents
children aef632415d11
files tag.xml
diffstat 1 files changed, 50 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tag.xml	Fri Jun 19 18:05:17 2020 -0400
@@ -0,0 +1,50 @@
+<tool id="tag" name="TAG in FASTA" version="0.1.0">
+  <description>Substituir nome por tags em sequências FASTA</description>
+    <command interpreter="python"> tag.py
+	#for $q in $inputs:
+	    ${q.arquivo} 
+	    ${q.tag}
+   	#end for
+    </command>
+    <inputs>
+	<repeat name="inputs" title="Proteome" min="1">
+       	   <param type="data" name="arquivo" format="fasta" label="Arquivo" help="Dataset" />
+	   <param type="text" name="tag" format="txt" label="TAG" help="Tag para o arquivo acima" />
+    	</repeat>
+    </inputs>
+     <outputs>
+ 	<data format="fasta" name="saida" label="${tool.name} Saída on: ${on_string}"  >
+            <discover_datasets pattern="(?P&lt;result_tag&gt;.*)" ext="fasta" visible="true" assign_primary_output="true" />
+	</data>
+     </outputs>
+<help>
+**Funcionamento**
+
+Substitui o nome completo da sequência por uma tag (informada) e o id da sequência (mantido)
+
+----
+
+**Output - Exemplo:**
+
+**Entrada:**
+
+	**&gt;CDI73658.1 hypothetical protein EPH_0011120 [Eimeria praecox]**
+	MGHPDSGFQGSANMTVVASELYNSIAAGKGETGELNFVFSPFSILSVFKMAQMGARGATRAEMDRHLSSSAPLDVPALRG
+	PAAPWETEPPIELETANRMYVKSSLASDAQFLHFASEVLAKLKCEAVTADFTDSEATAASINAFVEEKTKGHIKELVPAS
+	LLTSYTRMVLVNALYFKGPWAFPFSPESTSLGSFCMKDGETGCIHEQQVKFMRQRLDMGFGYYEGETAKVLSLPYADYRF
+	SLYVFLPQDISQFEQQLLQRPEAIEELVSRVDSSSSSGLVLDLSMPLVKLPAEQNQVDLVEVYKRLGVRLMFDADEADFS
+	GISRNETLYVSSFLHQADLTWNEEGTEAAAATAMMIAAASAFIPKREISLAVDRPFLFQVRVRDTTNSHSLVLLAGRVID
+	AKAAQ
+
+**Saída:** (tag = EPRA)
+
+	**&gt;EPRA|CDI73658.1**
+	MGHPDSGFQGSANMTVVASELYNSIAAGKGETGELNFVFSPFSILSVFKMAQMGARGATRAEMDRHLSSSAPLDVPALRG
+	PAAPWETEPPIELETANRMYVKSSLASDAQFLHFASEVLAKLKCEAVTADFTDSEATAASINAFVEEKTKGHIKELVPAS
+	LLTSYTRMVLVNALYFKGPWAFPFSPESTSLGSFCMKDGETGCIHEQQVKFMRQRLDMGFGYYEGETAKVLSLPYADYRF
+	SLYVFLPQDISQFEQQLLQRPEAIEELVSRVDSSSSSGLVLDLSMPLVKLPAEQNQVDLVEVYKRLGVRLMFDADEADFS
+	GISRNETLYVSSFLHQADLTWNEEGTEAAAATAMMIAAASAFIPKREISLAVDRPFLFQVRVRDTTNSHSLVLLAGRVID
+	AKAAQ
+
+</help>
+</tool>