# HG changeset patch
# User ayllon
# Date 1410079343 14400
# Node ID 620741ec77ed686b10ea35fed7402aec8d2c553c
# Parent  52bf4368c7cfeb0894da95d048fdd2c2153dae2c
Deleted selected files

diff -r 52bf4368c7cf -r 620741ec77ed tcoffee.pl
--- a/tcoffee.pl	Sun Sep 07 04:42:15 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 52bf4368c7cf -r 620741ec77ed tcoffee.xml
--- a/tcoffee.xml	Sun Sep 07 04:42:15 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,111 +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>
-
-  <stdio>
-    <exit_code range="1:" level="fatal" description="Error" />
-  </stdio>
-
-</tool>