# HG changeset patch
# User ayllon
# Date 1412869303 14400
# Node ID 27eeff0c00e620978850df31d038fe906845097a
# Parent  d68cdb8a6465d72ee9f00b8eebd90f90699c5be0
Deleted selected files

diff -r d68cdb8a6465 -r 27eeff0c00e6 Installation.txt
--- a/Installation.txt	Thu Oct 09 11:41:09 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,29 +0,0 @@
-{\rtf1\ansi\ansicpg1252\cocoartf1038\cocoasubrtf360
-{\fonttbl\f0\fnil\fcharset0 Menlo-Regular;}
-{\colortbl;\red255\green255\blue255;\red166\green23\blue0;\red128\green18\blue178;}
-\paperw11900\paperh16840\margl1440\margr1440\vieww9000\viewh8400\viewkind0
-\pard\tx560\tx1120\tx1680\tx2240\tx2800\tx3360\tx3920\tx4480\tx5040\tx5600\tx6160\tx6720\tx7280\tx7840\tx8400\tx8960\tx9520\tx10080\tx10640\tx11200\tx11760\tx12320\tx12880\tx13440\tx14000\tx14560\tx15120\tx15680\tx16240\tx16800\tx17360\tx17920\tx18480\tx19040\tx19600\tx20160\tx20720\tx21280\tx21840\tx22400\tx22960\tx23520\tx24080\tx24640\tx25200\tx25760\tx26320\tx26880\tx27440\tx28000\tx28560\tx29120\tx29680\tx30240\tx30800\tx31360\tx31920\tx32480\tx33040\tx33600\tx34160\tx34720\tx35280\tx35840\tx36400\tx36960\tx37520\tx38080\tx38640\tx39200\tx39760\tx40320\tx40880\tx41440\tx42000\tx42560\tx43120\tx43680\tx44240\tx44800\tx45360\tx45920\tx46480\tx47040\tx47600\tx48160\tx48720\tx49280\tx49840\tx50400\tx50960\tx51520\tx52080\tx52640\tx53200\tx53760\tx54320\tx54880\tx55440\tx56000\ql\qnatural\pardirnatural
-
-\f0\fs22 \cf2 \CocoaLigature0 \
-Installation tutorial for T-Coffee wrapper.\
-\
-First, you create a new section in xml file called tool_conf.xml and you the next: \
-\
-<\cf0 section id=\cf3 "aligment"\cf0  name=\cf3 "Multiple Aligment"\cf2 >\cf0 \
-    \cf2 <\cf0 tool file=\cf3 "aligment_tcoffee/tcoffee.xml"\cf0  \cf2 />\cf0 \
-  \cf2 </\cf0 section\cf2 >\
-\
-\
-\
-\
-\
-Afterwards, in datatypes_conf.xml, add this:\
-\
-\cf0  \cf2 <\cf0 datatype extension=\cf3 "msf"\cf0  type=\cf3 "galaxy.datatypes.data:Text"\cf0  display_in_upload=\cf3 "true"\cf2 />\cf0 \
-    \cf2 <\cf0 datatype extension=\cf3 "clustalw"\cf0  type=\cf3 "galaxy.datatypes.data:Text"\cf0  display_in_upload=\cf3 "true"\cf2 />\cf0 \
-    \cf2 <\cf0 datatype extension=\cf3 "pir"\cf0  type=\cf3 "galaxy.datatypes.data:Text"\cf0  display_in_upload=\cf3 "true"\cf2 />\cf0 \
-    \cf2 <\cf0 datatype extension=\cf3 "ascii"\cf0  type=\cf3 "galaxy.datatypes.data:Text"\cf0  display_in_upload=\cf3 "true"\cf2 />\
-\
-\
-\
-Then, entry tools folder and create a folder. Into new folder, add files xml and pl. Finally, into the test-data folder, you add files name: "out3.fasta".}
\ No newline at end of file
diff -r d68cdb8a6465 -r 27eeff0c00e6 tcoffee.pl
--- a/tcoffee.pl	Thu Oct 09 11:41:09 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,67 +0,0 @@
-#!/usr/bin/perl -w
-
-# usage : perl script.pl <FASTA file> <method01> <method02> <method03> $dnd $msf_aln $clustalw_aln $pir_aln $fasta_aln $phylip $pir_seq $fasta_seq $score_ascii $score_html
-
-#Chain wich will contains the paramater -output with the formats
-my $outputFormat = "";
-#Chain wich will contains the paramater for the -newtree, if the user wants
-my $outputTree = "";
-#Chain wich will contains the method of alignment of the process
-my $total = "";
-#Array where place the names of the formats, for the flag -output
-my @formats = ("msf_aln", "clustalw_aln", "pir_aln", "fasta_aln", "phylip", "pir_seq", "fasta_seq", "score_ascii", "score_html");
-#Array with the inputs for the methods of alignments
-my @array = ($ARGV[1], $ARGV[2], $ARGV[3]);
-#Array where will be placed the output files wich the user generate
-my @files;
-
-#Firstly the input methods of alignments are saved, if they exists (they aren't none), in the chain total, separated by commas
-for (my $i = 0; $i < int(@array); $i++){
-  if ($array[$i] ne "None"){
-    $total.=$array[$i].",";
-  } 
-}
-
-#If the user has selected the option of the tree, the chain of the tree will contains the file for the tree
-if ($ARGV[4] ne "None") {
-  $outputTree = "-newtree ".$ARGV[4]." ";
-}
-
-#copy is a variable which save the file and the extension of each output file ([0]:file1.dat, [1]:extension_file1, [2]:file2.dat, [3]extension_file2, ...)
-my $copy = -1;
-@array = ($ARGV[5],$ARGV[6],$ARGV[7],$ARGV[8],$ARGV[9],$ARGV[10],$ARGV[11],$ARGV[12],$ARGV[13]);
-for (my $i = 0; $i < int(@array); $i++){
-  if ($array[$i] ne "None"){
-    $outputFormat.=$formats[$i].",";
-    $copy++;
-    $files[$copy]=$array[$i];
-    $copy++;
-    $files[$copy]=$formats[$i];
-  } 
-}
-
-#if $total contains some method, we added the flag, and remove the last comma
-if ($total ne "") {
-  chop($total);
-  $total = "-method ".$total;
-}
-
-#if $outputFormat contains some output, we added the flag, and remove the last comma
-#the outfile will be the first output file
-#tcoffee will generate a first file without extension, with the name indicated in -outfile, but the other files will be named like this first file and the extension of the format
-if ($outputFormat ne "") {
-  chop($outputFormat);
-  $outputFormat = "-output ".$outputFormat." -outfile $files[0]";
-}
-
-#execution of the tcoffee; if there are not any method or output, this chains will be empty, so anything will be ejecuted in that flag
-system("t_coffee $ARGV[0] $total $outputTree $outputFormat -quiet");
-
-#finally, as tcoffee added an extension, we have to change the extension of the files and delete it (but not from the first file, that do not add any extension)
-my $fi;
-if ($copy > 1) {
-  for (my $i = 2; $i < int(@files); $i+=2){
-      $fi = $files[0].".".$files[$i+1];
-      system ("mv $fi $files[$i]");
-  }
-}
diff -r d68cdb8a6465 -r 27eeff0c00e6 tcoffee.xml
--- a/tcoffee.xml	Thu Oct 09 11:41:09 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,171 +0,0 @@
-<tool id="T_coffee" name="T-COFFEE" version="10.00.r1613">
-  <description>multiple aligment</description>
-  <command interpreter="perl">
-    tcoffee.pl $input $method01 $method02 $method03 $dnd $msf_aln $clustalw_aln $pir_aln $fasta_aln $phylip $pir_seq $fasta_seq $score_ascii $score_html
-  </command>
-
-  <inputs>
-    <param format="fasta" name="input" type="data" label="Source file"/>
-    <param name="method01" type="select" display="checkboxes" multiple="true" label="Pairwise Structual Method">
-        <option value="sap_pair">sap_pair</option>
-        <option value="TMalign_pair">TMalign_pair</option>
-        <option value="mustang_pair">mustang_pair</option>
-    </param>
-    <param name="method02" type="select" display="checkboxes" multiple="true" label="Multiple Sequence Alignment Methods">
-        <option value="pcma_msa">pcma_msa</option>
-        <option value="clustalw_msa">clustalw_msa</option>
-        <option value="dialigntx_msa">dialigntx_msa</option>
-        <option value="poa_msa">poa_msa</option>
-        <option value="muscle_msa">muscle_msa</option>
-        <option value="probcons_msa">probcons_msa</option>
-        <option value="t_coffee_msa">t_coffee_msa</option>
-        <option value="amap_msa">amap_msa</option>
-        <option value="kalign_msa">kalign_msa</option>
-    </param>
-    <param name="method03" type="select" display="checkboxes" multiple="true" label="Pairwise Sequence Alignment Methods">
-        <option value="fast_pair">fast_pair</option>
-        <option value="clustalw_pair">clustalw_pair</option>
-        <option value="lalign_id_pair">lalign_id_pair</option>
-        <option value="slow_pair">slow_pair</option>
-        <option value="proba_pair">proba_pair</option>
-    </param>
-    <param name="format_output_dnd" type="select" display="radio" label="Output newick">
-        <option value="no">No</option>
-        <option value="yes">Yes</option>
-    </param>
-    <param name="format_output_msf_aln" type="select" display="radio" label="Output msf_aln">
-        <option value="no">No</option>
-        <option value="yes">Yes</option>
-    </param>
-    <param name="format_output_clustalw_aln" type="select" display="radio" label="Output clustalw_aln">
-        <option value="no">No</option>
-        <option value="yes">Yes</option>
-    </param>
-    <param name="format_output_pir_aln" type="select" display="radio" label="Output pir_aln">
-        <option value="no">No</option>
-        <option value="yes">Yes</option>
-    </param>
-    <param name="format_output_fasta_aln" type="select" display="radio" label="Output fasta_aln">
-        <option value="no">No</option>
-        <option value="yes">Yes</option>
-    </param>
-    <param name="format_output_phylip" type="select" display="radio" label="Output phylip">
-        <option value="no">No</option>
-        <option value="yes">Yes</option>
-    </param>
-    <param name="format_output_pir_seq" type="select" display="radio" label="Output pir_seq">
-        <option value="no">No</option>
-        <option value="yes">Yes</option>
-    </param>
-    <param name="format_output_fasta_seq" type="select" display="radio" label="Output fasta_seq">
-        <option value="no">No</option>
-        <option value="yes">Yes</option>
-    </param>
-    <param name="format_output_score_ascii" type="select" display="radio" label="Output score_ascii">
-        <option value="no">No</option>
-        <option value="yes">Yes</option>
-    </param>
-    <param name="format_output_score_html" type="select" display="radio" label="Output score_html">
-        <option value="no">No</option>
-        <option value="yes">Yes</option>
-    </param>
-  </inputs>
-
-  <outputs>
-    <data format="nhx" name="dnd" label="${tool.name} on ${on_string}: newick.dnd" >
-      <filter>format_output_dnd == "yes"</filter>
-    </data>
-    <data format="msf" name="msf_aln" label="${tool.name} on ${on_string}: msf_aln" >
-      <filter>format_output_msf_aln == "yes"</filter>
-    </data>
-    <data format="clustalw" name="clustalw_aln" label="${tool.name} on ${on_string}: clustalw_aln" >
-      <filter>format_output_clustalw_aln == "yes"</filter>
-    </data>
-    <data format="pir" name="pir_aln" label="${tool.name} on ${on_string}: pir_aln" >
-      <filter>format_output_pir_aln == "yes"</filter>
-    </data>
-    <data format="fasta" name="fasta_aln" label="${tool.name} on ${on_string}: fasta_aln" >
-      <filter>format_output_fasta_aln == "yes"</filter>
-    </data>
-    <data format="phyloxml" name="phylip" label="${tool.name} on ${on_string}: phylip" >
-      <filter>format_output_phylip == "yes"</filter>
-    </data>
-    <data format="pir" name="pir_seq" label="${tool.name} on ${on_string}: pir_seq" >
-      <filter>format_output_pir_seq == "yes"</filter>
-    </data>
-    <data format="fasta" name="fasta_seq" label="${tool.name} on ${on_string}: fasta_seq" >
-      <filter>format_output_fasta_seq == "yes"</filter>
-    </data>
-    <data format="ascii" name="score_ascii" label="${tool.name} on ${on_string}: score_ascii" >
-      <filter>format_output_score_ascii == "yes"</filter>
-    </data>
-    <data format="html" name="score_html" label="${tool.name} on ${on_string}: score_html" >
-      <filter>format_output_score_html == "yes"</filter>
-    </data>
-  </outputs>
-  <help>
-    
-    **Requeriments**
-   
-    You must install T_coffee version "10.00.r1613" in your computer.
-   
------
-   
-    **What it does**
-
-    This tool is a wrapper for the T-Coffee multiple alignment suite. The input is a set of sequences in FASTA format that must be uploaded to Galaxy if not obtained using Galaxy tools.
-   
-    This wrapper offers selected advanced T-Coffee options like the selection of the alignment methods to use: ''Pairwise Structual Method'', ''Multiple Sequence Alignment
-    Methods'' or ''Pairwise Sequence Alignment Methods''.
-   
-     The T-Coffee documentation can be found at http://www.tcoffee.org/Projects/tcoffee/documentation
-   
------
-
-    **Example**
-
-    Suppose you have five sequences in FASTA format:
-
-      >1aboA
-      NLFVALYDFVASGDNTLSITKGEKLRVLGYNHNGEWCEAQTKNGQGWVPS
-      NYITPVN
-     
-      >1ycsB
-      KGVIYALWDYEPQNDDELPMKEGDCMTIIHREDEDEIEWWWARLNDKEGY
-      VPRNLLGLYP
-     
-      >1pht
-      GYQYRALYDYKKEREEDIDLHLGDILTVNKGSLVALGFSDGQEARPEEIG
-      WLNGYNETTGERGDFPGTYVEYIGRKKISP
-     
-      >1vie
-      DRVRKKSGAAWQGQIVGWYCTNLTPEGYAVESEAHPGSVQIYPVAALERI
-      N
-     
-      >1ihvA
-      NFRVYYRDSRDPVWKGPAKLLWKGEGAVVIQDNSDIKVVPRRKAKIIRD
-   
-     By selecting "yes" in output fasta_aln in the wrapper, the user will obtain the multiple alignment in FASTA format:
-
-      >1aboA
-      NL-FVA---LYDFVASGDNTLSITKGEKLR-------VLGYN-------H
-      NGEWCEA--QTKN-GQGWVPSNYIT------PVN
-      >1ycsB
-      KGVIYA---LWDYEPQNDDELPMKEGDCMT-------IIHREDE-----D
-      EIEWWWA--RLND-KEGYVPRNLLG------LYP
-      >1pht
-      GYQYRA---LYDYKKEREEDIDLHLGDILTVNKGSLVALGFSDGQEARPE
-      EIGWLNGYNETTG-ERGDFPGTYVEYIGRKKISP
-      >1vie
-      DR-----------VRK--KSGAAWQGQIVGWYCTNLTPEGYAVE------
-      ------S--EAHPGSVQIYPVAALE------RIN
-      >1ihvA
-      NF-RVYYRDSRDPVWKGPA-KLLWKGEGAV-------VIQDN-------S
-      DI--------------KVVPRRKAK-----IIRD
-      
-      </help>
-  <stdio>
-    <exit_code range="1:" level="fatal" description="Error" />
-  </stdio>
-
-</tool>