# HG changeset patch
# User bebatut
# Date 1460444079 14400
# Node ID 2f0a6f227f873f3d223377c5b62cb8b60f20366f
# Parent  617a5f3baf7f2bec1a892847590cb50cb774465f
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty

diff -r 617a5f3baf7f -r 2f0a6f227f87 cd_hit_est.xml
--- a/cd_hit_est.xml	Mon Dec 14 04:19:46 2015 -0500
+++ b/cd_hit_est.xml	Tue Apr 12 02:54:39 2016 -0400
@@ -1,87 +1,99 @@
 <tool id="cd_hit_est" name="CD-HIT-EST" version="1.2">
- <description>Cluster a nucleotide dataset into representative sequences</description>
- <requirements>
-  <requirement type="package" version="4.6.1">cd-hit</requirement>
- </requirements>
+  <description>Cluster a nucleotide dataset into representative sequences</description>
+
   <macros>
     <import>cdhit_macros.xml</import>
   </macros>
- <command>
-  cd-hit-est -i "$fasta_in" -o rep_seq -c $similarity -n $wordsize $strand
-  #include source=$common_cdhit_options#
-  #include source=$runtime_tuning#
- </command>
- <inputs>
-  <param name="fasta_in" type="data" format="fasta" label="EST Sequences to cluster"/>
-  <param name="similarity" type="float" value="0.9"  label="similarity threshold: .75 - 1.0, default is .9">
-    <validator type="in_range" message="sequence similarity threshold should be .75 - 1.0" min=".75" max="1.0"/>
-  </param>
-  <param name="wordsize" type="integer" value="8"  label="word size">
-    <help> Suggested word size:
-          8,9,10 for thresholds 0.90 ~ 1.0
-          7      for thresholds 0.88 ~ 0.9
-          6      for thresholds 0.85 ~ 0.88
-          5      for thresholds 0.80 ~ 0.85
-          4      for thresholds 0.75 ~ 0.8 
-    </help>
-    <validator type="in_range" message="word size should be between 4 and 10" min="4" max="10"/>
-  </param>
-  <param name="strand" type="boolean" truevalue="-r 1" falsevalue="" checked="false" label="Compare both strands"/>
-  <expand macro="common_cdhit_options" />
-  <expand macro="runtime_tuning" />
- </inputs>
- <outputs>
-  <data format="txt" name="clusters_out" label="${tool.name} on ${on_string}: clusters" from_work_dir="rep_seq.clstr"/>
-  <data format="fasta" name="fasta_out" label="${tool.name} on ${on_string}: representatives.fasta" from_work_dir="rep_seq"/>
- </outputs>
- <tests>
-  <test>
-    <!-- Expect 3 clusters: 0,1,2 -->
-    <param name="fasta_in" value="cd_hit_est_in.fa" />
-    <param name="similarity" value="0.9"/>
-    <param name="wordsize" value="8"/>
-    <param name="strand" value="true"/>
-    <!-- conditionals in macros -->
-    <param name="settings" value="no"/>
-    <param name="tuning" value="default"/>
-    <output name="clusters_out">
-        <assert_contents>
-            <has_text text=">Cluster 0" />
-            <!-- There should not be a Cluster 3 -->
-            <not_has_text text="Cluster 3" />
-            <has_text_matching expression="F12Fcsw_481739" />
-        </assert_contents>
-    </output>
-    <output name="fasta_out">
-        <assert_contents>
-            <has_text_matching expression="^>[MF]\d\dFcsw_\d*" />
-        </assert_contents>
-    </output>
-  </test>
-  <test>
-    <!-- tighter constraints should yield more clusters -->
-    <param name="fasta_in" value="cd_hit_est_in.fa" />
-    <param name="similarity" value="0.95"/>
-    <param name="wordsize" value="9"/>
-    <param name="strand" value="true"/>
-    <!-- conditionals in macros -->
-    <param name="settings" value="no"/>
-    <param name="tuning" value="default"/>
-    <output name="clusters_out">
-        <assert_contents>
-            <has_text text=">Cluster 4" />
-            <has_text_matching expression=">F12Fcsw_481739" />
-        </assert_contents>
-    </output>
-    <output name="fasta_out">
-        <assert_contents>
-            <has_text_matching expression="^>[MF]\d\dFcsw_\d*" />
-        </assert_contents>
-    </output>
-  </test>
- </tests>
- <help>
-**CD-HIT-EST**
+
+  <requirements>
+    <requirement type="package" version="4.6.1">cd-hit</requirement>
+  </requirements>
+
+  <command><![CDATA[
+    cd-hit-est
+      -i "$fasta_in" 
+      -o rep_seq 
+      -c $similarity 
+      -n $wordsize $strand
+   
+      #include source=$common_cdhit_options#
+      #include source=$runtime_tuning#
+  ]]></command>
+  
+  <inputs>
+    <param name="fasta_in" type="data" format="fasta" label="EST Sequences to cluster"/>
+    <param name="similarity" type="float" value="0.9"  label="similarity threshold: .75 - 1.0, default is .9">
+      <validator type="in_range" message="sequence similarity threshold should be .75 - 1.0" min=".75" max="1.0"/>
+    </param>
+    <param name="wordsize" type="integer" value="8"  label="word size">
+      <help> Suggested word size:
+             8,9,10 for thresholds 0.90 ~ 1.0
+             7      for thresholds 0.88 ~ 0.9
+             6      for thresholds 0.85 ~ 0.88
+             5      for thresholds 0.80 ~ 0.85
+             4      for thresholds 0.75 ~ 0.8 
+      </help>
+      <validator type="in_range" message="word size should be between 4 and 10" min="4" max="10"/>
+    </param>
+    <param name="strand" type="boolean" truevalue="-r 1" falsevalue="" checked="false" label="Compare both strands"/>
+    <expand macro="common_cdhit_options" />
+    <expand macro="runtime_tuning" />
+  </inputs>
+
+  <outputs>
+    <data format="txt" name="clusters_out" label="${tool.name} on ${on_string}: clusters" from_work_dir="rep_seq.clstr"/>
+    <data format="fasta" name="fasta_out" label="${tool.name} on ${on_string}: representatives.fasta" from_work_dir="rep_seq"/>
+  </outputs>
+  
+  <tests>
+   <test>
+     <!-- Expect 3 clusters: 0,1,2 -->
+     <param name="fasta_in" value="cd_hit_est_in.fa" />
+     <param name="similarity" value="0.9"/>
+     <param name="wordsize" value="8"/>
+     <param name="strand" value="true"/>
+     <!-- conditionals in macros -->
+     <param name="settings" value="no"/>
+     <param name="tuning" value="default"/>
+     <output name="clusters_out">
+         <assert_contents>
+             <has_text text=">Cluster 0" />
+             <!-- There should not be a Cluster 3 -->
+             <not_has_text text="Cluster 3" />
+             <has_text_matching expression="F12Fcsw_481739" />
+         </assert_contents>
+     </output>
+     <output name="fasta_out">
+         <assert_contents>
+             <has_text_matching expression="^>[MF]\d\dFcsw_\d*" />
+         </assert_contents>
+     </output>
+   </test>
+   <test>
+     <!-- tighter constraints should yield more clusters -->
+     <param name="fasta_in" value="cd_hit_est_in.fa" />
+     <param name="similarity" value="0.95"/>
+     <param name="wordsize" value="9"/>
+     <param name="strand" value="true"/>
+     <!-- conditionals in macros -->
+     <param name="settings" value="no"/>
+     <param name="tuning" value="default"/>
+     <output name="clusters_out">
+         <assert_contents>
+             <has_text text=">Cluster 4" />
+             <has_text_matching expression=">F12Fcsw_481739" />
+         </assert_contents>
+     </output>
+     <output name="fasta_out">
+         <assert_contents>
+             <has_text_matching expression="^>[MF]\d\dFcsw_\d*" />
+         </assert_contents>
+     </output>
+   </test>
+  </tests>
+
+  <help><![CDATA[
+**What it does**
 
 CD-HIT_ stands for Cluster Database at High Identity with Tolerance. The program (cd-hit) takes a fasta format sequence database as input and produces a set of 'non-redundant' (nr) representative sequences as output. In addition cd-hit outputs a cluster file, documenting the sequence 'groupies' for each nr sequence representative. The idea is to reduce the overall size of the database without removing any sequence information by only removing 'redundant' (or highly similar) sequences. This is why the resulting database is called non-redundant (nr). Essentially, cd-hit produces a set of closely related protein families from a given fasta sequence database.
 
@@ -116,5 +128,10 @@
 	3 2208aa, >PF06317.1|RRPO_TACV/1-2208... at 69%
 
 
- </help>
+  ]]></help>
+
+  <citations>
+    <citation type="doi">10.1093/bioinformatics/btl158</citation>
+    <citation type="doi">10.1093/bioinformatics/bts565</citation>
+  </citations>
 </tool>
diff -r 617a5f3baf7f -r 2f0a6f227f87 cd_hit_protein.xml
--- a/cd_hit_protein.xml	Mon Dec 14 04:19:46 2015 -0500
+++ b/cd_hit_protein.xml	Tue Apr 12 02:54:39 2016 -0400
@@ -1,82 +1,92 @@
 <tool id="cd_hit_protein" name="CD-HIT PROTEIN" version="1.2">
- <description>Cluster a protein dataset into representative sequences</description>
- <requirements>
-  <requirement type="package" version="4.6.1">cd-hit</requirement>
- </requirements>
+  <description>Cluster a protein dataset into representative sequences</description>
+
   <macros>
     <import>cdhit_macros.xml</import>
   </macros>
- <command>
-  cd-hit -i "$fasta_in" -o rep_seq -c $similarity -n $wordsize 
-  #include source=$common_cdhit_options#
-  #include source=$runtime_tuning#
- </command>
- <inputs>
-  <param name="fasta_in" type="data" format="fasta" label="Protein Sequences to cluster"/>
-  <param name="similarity" type="float" value="0.9"  label="similarity threshold: .4 - 1.0 (default .9)">
-    <validator type="in_range" message="sequence similarity threshold should be .4 - 1.0" min=".4" max="1.0"/>
-  </param>
-  <param name="wordsize" type="integer" value="5"  label="word size (default 5)">
-    <help> Suggested word size:
-          5    for thresholds 0.7 ~ 1.0; 
-          4    for thresholds 0.6 ~ 0.7; 
-          3    for thresholds 0.5 ~ 0.6; 
-          2    for thresholds 0.4 ~ 0.5; 
-    </help>
-    <validator type="in_range" message="word size should be between 2 and 5" min="2" max="5"/>
-  </param>
-  <expand macro="common_cdhit_options" />
-  <expand macro="runtime_tuning" />
- </inputs>
- <outputs>
-  <data format="txt" name="clusters_out" label="${tool.name} on ${on_string}: clusters" from_work_dir="rep_seq.clstr"/>
-  <data format="fasta" name="fasta_out" label="${tool.name} on ${on_string}: representatives.fasta" from_work_dir="rep_seq"/>
- </outputs>
- <tests>
-  <test>
-    <param name="fasta_in" value="cd_hit_protein_in.fasta" />
-    <param name="similarity" value="0.9"/>
-    <param name="wordsize" value="5"/>
-    <!-- conditionals in macros -->
-    <param name="settings" value="no"/>
-    <param name="tuning" value="default"/>
-    <output name="clusters_out">
+
+  <requirements>
+    <requirement type="package" version="4.6.1">cd-hit</requirement>
+  </requirements>
+
+  <command><![CDATA[
+    cd-hit 
+      -i "$fasta_in" 
+      -o rep_seq 
+      -c $similarity 
+      -n $wordsize 
+      #include source=$common_cdhit_options#
+      #include source=$runtime_tuning#
+  ]]></command>
+
+  <inputs>
+    <param name="fasta_in" type="data" format="fasta" label="Protein Sequences to cluster"/>
+    <param name="similarity" type="float" value="0.9"  label="similarity threshold: .4 - 1.0 (default .9)">
+      <validator type="in_range" message="sequence similarity threshold should be .4 - 1.0" min=".4" max="1.0"/>
+    </param>
+    <param name="wordsize" type="integer" value="5"  label="word size (default 5)">
+      <help> Suggested word size:
+           5    for thresholds 0.7 ~ 1.0; 
+           4    for thresholds 0.6 ~ 0.7; 
+           3    for thresholds 0.5 ~ 0.6; 
+           2    for thresholds 0.4 ~ 0.5; 
+      </help>
+      <validator type="in_range" message="word size should be between 2 and 5" min="2" max="5"/>
+    </param>
+    <expand macro="common_cdhit_options" />
+    <expand macro="runtime_tuning" />
+  </inputs>
+
+  <outputs>
+    <data format="txt" name="clusters_out" label="${tool.name} on ${on_string}: clusters" from_work_dir="rep_seq.clstr"/>
+    <data format="fasta" name="fasta_out" label="${tool.name} on ${on_string}: representatives.fasta" from_work_dir="rep_seq"/>
+  </outputs>
+
+  <tests>
+    <test>
+       <param name="fasta_in" value="cd_hit_protein_in.fasta" />
+       <param name="similarity" value="0.9"/>
+       <param name="wordsize" value="5"/>
+       <!-- conditionals in macros -->
+       <param name="settings" value="no"/>
+       <param name="tuning" value="default"/>
+       <output name="clusters_out">
+           <assert_contents>
+               <has_text text="Cluster 0" />
+               <!--
+               <has_text_matching expression=">sp.P00338-2.LDHA_HU" />
+               -->
+           </assert_contents>
+       </output>
+       <output name="fasta_out">
+           <assert_contents>
+               <has_text_matching expression=">sp.P19858.LDHA_BOVIN" />
+           </assert_contents>
+       </output>
+    </test>
+    <test>
+      <param name="fasta_in" value="cd_hit_protein_in.fasta" />
+      <param name="similarity" value="0.8" />
+      <param name="wordsize" value="5" />
+     <!-- conditionals in macros -->
+      <param name="settings" value="no"/>
+      <param name="tuning" value="default"/>
+      <output name="clusters_out">
         <assert_contents>
-            <has_text text="Cluster 0" />
-            <!--
-            <has_text_matching expression=">sp.P00338-2.LDHA_HU" />
-            -->
-        </assert_contents>
-    </output>
-    <output name="fasta_out">
-        <assert_contents>
-            <has_text_matching expression=">sp.P19858.LDHA_BOVIN" />
+      <has_text text="Cluster 0" />
+      <not_has_text text="Cluster 4" />
         </assert_contents>
-    </output>
-  </test>
-  <test>
-    <param name="fasta_in" value="cd_hit_protein_in.fasta" />
-    <param name="similarity" value="0.8" />
-    <param name="wordsize" value="5" />
-    <!-- conditionals in macros -->
-    <param name="settings" value="no"/>
-    <param name="tuning" value="default"/>
-    <output name="clusters_out">
-      <assert_contents>
-	<has_text text="Cluster 0" />
-	<not_has_text text="Cluster 4" />
-      </assert_contents>
-    </output>
-    <output name="fasta_out">
-      <assert_contents>
-	<has_text_matching expression=">sp.P00340.LDHA_CHICK" />
-      </assert_contents>
-    </output>
-  </test>
- </tests>
+      </output>
+      <output name="fasta_out">
+        <assert_contents>
+        <has_text_matching expression=">sp.P00340.LDHA_CHICK" />
+        </assert_contents>
+      </output>
+    </test>
+  </tests>
 
- <help>
-**CD-HIT**
+  <help><![CDATA[
+**What it does**
 
 CD-HIT_ stands for Cluster Database at High Identity with Tolerance. The program (cd-hit) takes a fasta format sequence database as input and produces a set of 'non-redundant' (nr) representative sequences as output. In addition cd-hit outputs a cluster file, documenting the sequence 'groupies' for each nr sequence representative. The idea is to reduce the overall size of the database without removing any sequence information by only removing 'redundant' (or highly similar) sequences. This is why the resulting database is called non-redundant (nr). Essentially, cd-hit produces a set of closely related protein families from a given fasta sequence database.
 
@@ -111,5 +121,10 @@
 	3 2208aa, >PF06317.1|RRPO_TACV/1-2208... at 69%
 
 
- </help>
+  ]]></help>
+
+  <citations>
+    <citation type="doi">10.1093/bioinformatics/btl158</citation>
+    <citation type="doi">10.1093/bioinformatics/bts565</citation>
+  </citations>
 </tool>