From c5aa37fd91c01410b033e11458915c5dfc8ea83f Mon Sep 17 00:00:00 2001
From: Chinmay Rao <chinmay@bx.psu.edu>
Date: Tue, 11 Dec 2007 16:31:09 +0000
Subject: [PATCH] Upgrading EMBOSS tools btwsited, cai, custom cai and chaos to
 version 5.0

---
 tools/emboss_5/emboss_btwisted.xml   |  23 ++++
 tools/emboss_5/emboss_cai.xml        | 184 +++++++++++++++++++++++++++
 tools/emboss_5/emboss_cai_custom.xml |  26 ++++
 tools/emboss_5/emboss_chaos.xml      |  22 ++++
 4 files changed, 255 insertions(+)
 create mode 100644 tools/emboss_5/emboss_btwisted.xml
 create mode 100644 tools/emboss_5/emboss_cai.xml
 create mode 100644 tools/emboss_5/emboss_cai_custom.xml
 create mode 100644 tools/emboss_5/emboss_chaos.xml

diff --git a/tools/emboss_5/emboss_btwisted.xml b/tools/emboss_5/emboss_btwisted.xml
new file mode 100644
index 00000000000..748c49a424d
--- /dev/null
+++ b/tools/emboss_5/emboss_btwisted.xml
@@ -0,0 +1,23 @@
+<tool id="EMBOSS_btwisted5" name="btwisted">
+  <description>Calculates the twisting in a B-DNA sequence</description>
+  <command>btwisted -sequence $input1 -outfile $out_file1 -auto</command>
+  <inputs>
+    <param format="data" name="input1" type="data">
+      <label>On query</label>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="btwisted" name="out_file1" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="input1" value="2.fasta"/>
+      <output name="out_file1" file="emboss_btwisted_out.btwisted"/>
+    </test>
+  </tests>
+  <help>
+    You can view the original documentation here_.
+    
+    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/btwisted.html
+  </help>
+</tool>
\ No newline at end of file
diff --git a/tools/emboss_5/emboss_cai.xml b/tools/emboss_5/emboss_cai.xml
new file mode 100644
index 00000000000..058b4dbc8bb
--- /dev/null
+++ b/tools/emboss_5/emboss_cai.xml
@@ -0,0 +1,184 @@
+<tool id="EMBOSS_cai6" name="cai">
+  <description>CAI codon adaptation index</description>
+  <command>cai -seqall $input1 -outfile $out_file1 -cfile $cfile -auto</command>
+  <inputs>
+    <param format="fasta" name="input1" type="data">
+      <label>On query</label>
+    </param>
+    <param name="cfile" type="select">
+      <label>Codon Usage File</label>
+      <option value="Eyeastcai.cut">Eyeastcai.cut</option>
+      <option value="Ehum.cut">Ehum.cut</option>
+      <option value="Eacc.cut">Eacc.cut</option>
+      <option value="Eadenovirus5.cut">Eadenovirus5.cut</option>
+      <option value="Eadenovirus7.cut">Eadenovirus7.cut</option>
+      <option value="Eaidlav.cut">Eaidlav.cut</option>
+      <option value="Eanasp.cut">Eanasp.cut</option>
+      <option value="Eani.cut">Eani.cut</option>
+      <option value="Eani_h.cut">Eani_h.cut</option>
+      <option value="Eanidmit.cut">Eanidmit.cut</option>
+      <option value="Easn.cut">Easn.cut</option>
+      <option value="Eath.cut">Eath.cut</option>
+      <option value="Eatu.cut">Eatu.cut</option>
+      <option value="Eavi.cut">Eavi.cut</option>
+      <option value="Ebja.cut">Ebja.cut</option>
+      <option value="Ebly.cut">Ebly.cut</option>
+      <option value="Ebme.cut">Ebme.cut</option>
+      <option value="Ebmo.cut">Ebmo.cut</option>
+      <option value="Ebna.cut">Ebna.cut</option>
+      <option value="Ebov.cut">Ebov.cut</option>
+      <option value="Ebovsp.cut">Ebovsp.cut</option>
+      <option value="Ebst.cut">Ebst.cut</option>
+      <option value="Ebsu.cut">Ebsu.cut</option>
+      <option value="Ebsu_h.cut">Ebsu_h.cut</option>
+      <option value="Ecac.cut">Ecac.cut</option>
+      <option value="Ecal.cut">Ecal.cut</option>
+      <option value="Eccr.cut">Eccr.cut</option>
+      <option value="Ecel.cut">Ecel.cut</option>
+      <option value="Echi.cut">Echi.cut</option>
+      <option value="Echicken.cut">Echicken.cut</option>
+      <option value="Echisp.cut">Echisp.cut</option>
+      <option value="Echk.cut">Echk.cut</option>
+      <option value="Echmp.cut">Echmp.cut</option>
+      <option value="Echnt.cut">Echnt.cut</option>
+      <option value="Echos.cut">Echos.cut</option>
+      <option value="Echzm.cut">Echzm.cut</option>
+      <option value="Echzmrubp.cut">Echzmrubp.cut</option>
+      <option value="Ecpx.cut">Ecpx.cut</option>
+      <option value="Ecre.cut">Ecre.cut</option>
+      <option value="Ecrisp.cut">Ecrisp.cut</option>
+      <option value="Ectr.cut">Ectr.cut</option>
+      <option value="Edayhoff.cut">Edayhoff.cut</option>
+      <option value="Eddi.cut">Eddi.cut</option>
+      <option value="Eddi_h.cut">Eddi_h.cut</option>
+      <option value="Edog.cut">Edog.cut</option>
+      <option value="Edro.cut">Edro.cut</option>
+      <option value="Edro_h.cut">Edro_h.cut</option>
+      <option value="Edrosophila.cut">Edrosophila.cut</option>
+      <option value="Eeca.cut">Eeca.cut</option>
+      <option value="Eeco.cut">Eeco.cut</option>
+      <option value="Eeco_h.cut">Eeco_h.cut</option>
+      <option value="Eecoli.cut">Eecoli.cut</option>
+      <option value="Ef1.cut">Ef1.cut</option>
+      <option value="Efish.cut">Efish.cut</option>
+      <option value="Efmdvpolyp.cut">Efmdvpolyp.cut</option>
+      <option value="Eham.cut">Eham.cut</option>
+      <option value="Ehha.cut">Ehha.cut</option>
+      <option value="Ehin.cut">Ehin.cut</option>
+      <option value="Ehma.cut">Ehma.cut</option>
+      <option value="Ehuman.cut">Ehuman.cut</option>
+      <option value="Ekla.cut">Ekla.cut</option>
+      <option value="Ekpn.cut">Ekpn.cut</option>
+      <option value="Ella.cut">Ella.cut</option>
+      <option value="Emac.cut">Emac.cut</option>
+      <option value="Emaize.cut">Emaize.cut</option>
+      <option value="Emam_h.cut">Emam_h.cut</option>
+      <option value="Emixlg.cut">Emixlg.cut</option>
+      <option value="Emouse.cut">Emouse.cut</option>
+      <option value="Emsa.cut">Emsa.cut</option>
+      <option value="Emse.cut">Emse.cut</option>
+      <option value="Emta.cut">Emta.cut</option>
+      <option value="Emtu.cut">Emtu.cut</option>
+      <option value="Emus.cut">Emus.cut</option>
+      <option value="Emussp.cut">Emussp.cut</option>
+      <option value="Emva.cut">Emva.cut</option>
+      <option value="Emze.cut">Emze.cut</option>
+      <option value="Emzecp.cut">Emzecp.cut</option>
+      <option value="Encr.cut">Encr.cut</option>
+      <option value="Eneu.cut">Eneu.cut</option>
+      <option value="Engo.cut">Engo.cut</option>
+      <option value="Eoncsp.cut">Eoncsp.cut</option>
+      <option value="Epae.cut">Epae.cut</option>
+      <option value="Epea.cut">Epea.cut</option>
+      <option value="Epet.cut">Epet.cut</option>
+      <option value="Epfa.cut">Epfa.cut</option>
+      <option value="Ephix174.cut">Ephix174.cut</option>
+      <option value="Ephv.cut">Ephv.cut</option>
+      <option value="Ephy.cut">Ephy.cut</option>
+      <option value="Epig.cut">Epig.cut</option>
+      <option value="Epolyomaa2.cut">Epolyomaa2.cut</option>
+      <option value="Epombe.cut">Epombe.cut</option>
+      <option value="Epombecai.cut">Epombecai.cut</option>
+      <option value="Epot.cut">Epot.cut</option>
+      <option value="Eppu.cut">Eppu.cut</option>
+      <option value="Epse.cut">Epse.cut</option>
+      <option value="Epsy.cut">Epsy.cut</option>
+      <option value="Epvu.cut">Epvu.cut</option>
+      <option value="Erab.cut">Erab.cut</option>
+      <option value="Erabbit.cut">Erabbit.cut</option>
+      <option value="Erabsp.cut">Erabsp.cut</option>
+      <option value="Erat.cut">Erat.cut</option>
+      <option value="Eratsp.cut">Eratsp.cut</option>
+      <option value="Erca.cut">Erca.cut</option>
+      <option value="Erhm.cut">Erhm.cut</option>
+      <option value="Eric.cut">Eric.cut</option>
+      <option value="Erle.cut">Erle.cut</option>
+      <option value="Erme.cut">Erme.cut</option>
+      <option value="Ersp.cut">Ersp.cut</option>
+      <option value="Esalsp.cut">Esalsp.cut</option>
+      <option value="Esau.cut">Esau.cut</option>
+      <option value="Esco.cut">Esco.cut</option>
+      <option value="Esgi.cut">Esgi.cut</option>
+      <option value="Eshp.cut">Eshp.cut</option>
+      <option value="Eshpsp.cut">Eshpsp.cut</option>
+      <option value="Esli.cut">Esli.cut</option>
+      <option value="Eslm.cut">Eslm.cut</option>
+      <option value="Esma.cut">Esma.cut</option>
+      <option value="Esmi.cut">Esmi.cut</option>
+      <option value="Esmu.cut">Esmu.cut</option>
+      <option value="Esoy.cut">Esoy.cut</option>
+      <option value="Espi.cut">Espi.cut</option>
+      <option value="Espn.cut">Espn.cut</option>
+      <option value="Espo.cut">Espo.cut</option>
+      <option value="Espo_h.cut">Espo_h.cut</option>
+      <option value="Espu.cut">Espu.cut</option>
+      <option value="Esta.cut">Esta.cut</option>
+      <option value="Esty.cut">Esty.cut</option>
+      <option value="Esus.cut">Esus.cut</option>
+      <option value="Esv40.cut">Esv40.cut</option>
+      <option value="Esyhsp.cut">Esyhsp.cut</option>
+      <option value="Esynsp.cut">Esynsp.cut</option>
+      <option value="Etbr.cut">Etbr.cut</option>
+      <option value="Etcr.cut">Etcr.cut</option>
+      <option value="Eter.cut">Eter.cut</option>
+      <option value="Etetsp.cut">Etetsp.cut</option>
+      <option value="Etob.cut">Etob.cut</option>
+      <option value="Etobcp.cut">Etobcp.cut</option>
+      <option value="Etom.cut">Etom.cut</option>
+      <option value="Etrb.cut">Etrb.cut</option>
+      <option value="Evco.cut">Evco.cut</option>
+      <option value="Ewht.cut">Ewht.cut</option>
+      <option value="Exel.cut">Exel.cut</option>
+      <option value="Exenopus.cut">Exenopus.cut</option>
+      <option value="Eyeast.cut">Eyeast.cut</option>
+      <option value="Eyen.cut">Eyen.cut</option>
+      <option value="Eysc.cut">Eysc.cut</option>
+      <option value="Eysc_h.cut">Eysc_h.cut</option>
+      <option value="Eyscmt.cut">Eyscmt.cut</option>
+      <option value="Eysp.cut">Eysp.cut</option>
+      <option value="Ezebrafish.cut">Ezebrafish.cut</option>
+      <option value="Ezma.cut">Ezma.cut</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="cai" name="out_file1" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="input1" value="2.fasta"/>
+      <param name="cfile" value="Eyeastcai.cut"/>
+      <output name="out_file1" file="emboss_cai_out.cai"/>
+    </test>
+  </tests>
+  <help>
+.. class:: warningmark
+
+The input dataset needs to be sequences.
+
+-----
+
+    You can view the original documentation here_.
+    
+    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/cai.html
+  </help>
+</tool>
diff --git a/tools/emboss_5/emboss_cai_custom.xml b/tools/emboss_5/emboss_cai_custom.xml
new file mode 100644
index 00000000000..5ff73e8d425
--- /dev/null
+++ b/tools/emboss_5/emboss_cai_custom.xml
@@ -0,0 +1,26 @@
+<tool id="EMBOSS: cai_custom6" name="cai custom">
+  <description>CAI codon adaptation index using custom codon usage file</description>
+  <command>cai -seqall $input1 -outfile $out_file1 -cfile $input2 -auto</command>
+  <inputs>
+    <param format="fasta" name="input1" type="data">
+      <label>On query</label>
+    </param>
+    <param format="txt" name="input2" type="data">
+      <label>Codon Usage File</label>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="txt" name="out_file1" />
+  </outputs>
+  <help>
+.. class:: warningmark
+
+The input dataset needs to be sequences.
+
+-----
+
+    You can view the original documentation here_.
+    
+    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/cai_custom.html
+  </help>
+</tool>
diff --git a/tools/emboss_5/emboss_chaos.xml b/tools/emboss_5/emboss_chaos.xml
new file mode 100644
index 00000000000..da7eed7c4b4
--- /dev/null
+++ b/tools/emboss_5/emboss_chaos.xml
@@ -0,0 +1,22 @@
+<tool id="EMBOSS_chaos7" name="chaos">
+  <description>Create a chaos game representation plot for a sequence</description>
+  <command interpreter="perl">emboss_single_outputfile_wrapper.pl chaos -sequence $input1 -graph png -goutfile $out_file1 -auto</command>
+  <inputs>
+    <param format="data" name="input1" type="data">
+      <label>On query</label>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="png" name="out_file1" />
+  </outputs>
+<!--    <tests>
+    <test>
+         puts name of file into the png
+    </test>
+  </tests> -->
+  <help>
+    You can view the original documentation here_.
+    
+    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/chaos.html
+  </help>
+</tool>
\ No newline at end of file