diff cmbuild.xml @ 8:c9e29ac5d099 draft default tip

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit a812ed8de433ac4e8b42afd636e70cfbb180d2b9"

--- a/cmbuild.xml	Sat Nov 11 16:01:09 2017 -0500
+++ b/cmbuild.xml	Thu Sep 23 19:38:58 2021 +0000
@@ -1,11 +1,12 @@
-<tool id="infernal_cmbuild" name="cmbuild" version="@VERSION@.0">
+<tool id="infernal_cmbuild" name="cmbuild" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>Build covariance models from sequence alignments</description>
     <macros>
         <import>macros.xml</import>
     </macros>
-    <parallelism method="multi" split_inputs="alignment_infile" split_mode="to_size" split_size="10" merge_outputs="cmfile_outfile"></parallelism>
+    <!--parallelism method="multi" split_inputs="alignment_infile" split_mode="to_size" split_size="10" merge_outputs="cmfile_outfile"></parallelism-->
     <expand macro="requirements" />
     <expand macro="stdio" />
+    <expand macro="xrefs"/>
     <command>
 <![CDATA[
     cmbuild
@@ -38,6 +39,9 @@
             #if $effective_opts.eminseq
                 --eminseq $effective_opts.eminseq
             #end if
+            #if $effective_opts.emaxseq
+                --emaxseq $effective_opts.emaxseq
+            #end if
             #if $effective_opts.ehmmre
                 --ehmmre $effective_opts.ehmmre
             #end if
@@ -151,6 +155,9 @@
                     <param name="eminseq" type="integer" value=""
                         label="Define the minimum allowed effective sequence number" help="(--eminseq)" optional="true"/>
 
+                    <param name="emaxseq" type="integer" value=""
+                    label="Define the maximum allowed effective sequence number" help="(--emaxseq)" optional="true"/>
+
                     <param name="ehmmre" type="float" value=""
                         label="Set the target HMM mean match state relative entropy" help="(--ehmmre)" optional="true"/>
 
@@ -253,7 +260,7 @@
 
         </inputs>
     <outputs>
-        <data format="text" name="summary_outfile" label="cmbuild summary on ${on_string}">
+        <data format="txt" name="summary_outfile" label="cmbuild summary on ${on_string}">
             <filter>is_summery_output is True</filter>
         </data>
         <!--<data format="stockholm" name="annotated_source_alignment_outfile" label="Annotated alignment from ${on_string}"/>-->
@@ -324,12 +331,29 @@
                 <param name="selector" value="true"/>
                 <param name="L" value="0.1"/>
             </conditional>
-            <output name="outfile">
+            <output name="cmfile_outfile">
                 <assert_contents>
                     <has_text text="S     0    -1 0     1     4     0     1    89   109  -7.220  -8.465  -0.063  -4.919"/>
                 </assert_contents>
             </output>
         </test>
+        <!-- Test emax seq parameter -->
+        <test>
+            <param name="alignment_infile" value="cmbuild_input_tRNA5.sto"/>
+            <conditional name="Calibrate">
+                <param name="selector" value="true"/>
+                <param name="L" value="0.1"/>
+            </conditional>
+            <conditional name="effective_opts">
+                <param name="effective_opts_selector" value="--eent"/>
+                <param name="emaxseq" value="100"/>
+            </conditional>
+            <output name="cmfile_outfile">
+                <assert_contents>
+                    <has_text text="S     0    -1 0     1     4     0     1    89   109  -7.111  -8.357  -0.068  -4.810"/>
+                </assert_contents>
+            </output>
+        </test>
     </tests>
     <help>
 <![CDATA[