diff maxbin2.xml @ 5:8a0473eb465e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e5b086199e53e32ffdf46ac6ba36c43f8ef6db26

--- a/maxbin2.xml	Wed Nov 18 10:42:37 2020 +0000
+++ b/maxbin2.xml	Fri Jun 17 17:27:40 2022 +0000
@@ -1,157 +1,202 @@
-<tool id="maxbin2" name="MaxBin2" version="@MAXBIN_VERSION@+galaxy2">
+<tool id="maxbin2" name="MaxBin2" version="@MAXBIN_VERSION@+galaxy3">
     <description>clusters metagenomic contigs into bins</description>
+    <xrefs>
+        <xref type="bio.tools">masigpro</xref>
+    </xrefs>
     <macros>
         <token name="@MAXBIN_VERSION@">2.2.7</token>
+        <xml name="contig">
+            <param argument="-contig" type="data" format="fasta,fasta.gz" label="Contig file"/>
+        </xml>
+        <xml name="input_type">
+            <param name="type" type="select" label="Input type">
+                <option value="reads" selected="true">Sequencing Reads</option>
+                <option value="abund">Abundances</option>
+            </param>
+        </xml>
+        <xml name="reads_extra_params">
+            <param name="output_abundances" type="boolean" checked="false" label="Output abundances" help="" />
+            <param argument="--reassembly" type="boolean" truevalue="-reassembly" falsevalue="" checked="false" label="Reassembly" help="Reassembly option is still highly experimental. To use this function, you need to feed MaxBin interleaved paired-end fastq or fasta file." />
+        </xml>
     </macros>
     <requirements>
         <requirement type="package" version="@MAXBIN_VERSION@">maxbin2</requirement>
     </requirements>
     <version_command><![CDATA[run_MaxBin.pl -version | head -n 1]]></version_command>
     <command detect_errors="exit_code"><![CDATA[
-    ## generate read or abundance files	
-    #if $intype_cond.intype_select == 'rds':
-        #for $r in $intype_cond.reads
+## generate read or abundance files
+#if $assembly.inputs.type == 'reads'
+    #if $assembly.type == 'individual'
+echo '$assembly.inputs.reads' >> reads_list &&
+    #else
+        #for $r in $assembly.inputs.reads
             #if $r
-                echo '$r' >> reads_list &&
+echo '$r' >> reads_list &&
             #end if
         #end for
-    #else if $intype_cond.intype_select == 'abdc':
-        #for $a in $intype_cond.abund
+    #end if
+#else if $assembly.inputs.type == 'abund'
+    #if $assembly.type == 'individual'
+echo '$assembly.inputs.abund' >> abund_list &&
+    #else
+        #for $a in $assembly.inputs.abund
             #if $a
-                echo '$a' >> abund_list &&
+echo '$a' >> abund_list &&
             #end if
         #end for
     #end if
+#end if
 
-    ## in case of reassembly the IBDA out and err is appended
-    ## to differentiate this a header is added also befor the
-    ## MaxBin2 outputs
-    #if $intype_cond.intype_select == 'rds' and $intype_cond.reassembly != ""
-        echo "==== MaxBin2 stdout ====" &&
-        echo "==== MaxBin2 stderr ====" 1>&2 &&
-    #end if
+## in case of reassembly the IBDA out and err is appended
+## to differentiate this a header is added also befor the
+## MaxBin2 outputs
+#if $assembly.inputs.type == 'reads' and $assembly.inputs.reassembly != ""
+echo "==== MaxBin2 stdout ====" &&
+echo "==== MaxBin2 stderr ====" 1>&2 &&
+#end if
 
-    run_MaxBin.pl
+run_MaxBin.pl
     -contig '$contig'
     -out out
-    #if $intype_cond.intype_select == 'rds':
-        -reads_list reads_list
-        $intype_cond.reassembly
-    #else if $intype_cond.intype_select == 'abdc':
-        -abund_list abund_list
-    #end if
-    #if $adv_cond.adv_select == 'yes':
-        -min_contig_length $adv_cond.min_contig_length
-        -max_iteration $adv_cond.max_iteration
-        -prob_threshold $adv_cond.prob_threshold
-        $adv_cond.plotmarker
-        -markerset $adv_cond.markerset
-    #end if
+#if $assembly.inputs.type == 'reads':
+    -reads_list reads_list
+    $assembly.inputs.reassembly
+#else if $assembly.inputs.type == 'abund':
+    -abund_list abund_list
+#end if
+    -min_contig_length $adv.min_contig_length
+    -max_iteration $adv.max_iteration
+    -prob_threshold $adv.prob_threshold
+    $output.plotmarker
+    -markerset $output.markerset
     -thread \${GALAXY_SLOTS:-1}
 
-    && gzip -cd out.marker_of_each_bin.tar.gz | tar -xf -
+&& gzip -cd out.marker_of_each_bin.tar.gz | tar -xf -
 
-    ## redirect the idba out and err file content to stdout and err
-    ## since this is also wanted in case the error case ';' is used here to 
-    ## separate commands
-    #if $intype_cond.intype_select == 'rds' and $intype_cond.reassembly != ""
-        ; echo "==== IDBA stdout ===="
-        && if [[ -f out.idba.out ]]; then cat out.idba.out; fi
-        && echo "==== IDBA stderr ====" 1>&2
-        && if [[ -f out.idba.err ]]; then cat out.idba.err 1>&2; fi
-    #end if
+## redirect the idba out and err file content to stdout and err
+## since this is also wanted in case the error case ';' is used here to
+## separate commands
+#if $assembly.inputs.type == 'reads' and $assembly.inputs.reassembly != ""
+; echo "==== IDBA stdout ===="
+&& if [[ -f out.idba.out ]]; then cat out.idba.out; fi
+&& echo "==== IDBA stderr ====" 1>&2
+&& if [[ -f out.idba.err ]]; then cat out.idba.err 1>&2; fi
+#end if
     ]]></command>
     <inputs>
-        <param argument="-contig" type="data" format="fasta,fasta.gz" label="Contig file"/>
-          <conditional name="intype_cond">
-              <param name="intype_select" type="select" label="Input type">
-                  <option value="rds" selected="true">Sequencing Reads</option>
-                  <option value="abdc">Abundances</option>
-              </param>
-              <when value="rds">
-                  <param name="reads" type="data" format="fasta,fastq" multiple="true" label="Reads file(s)" help="(-read/-read2/...)"/>
-                  <param name="output_abundances" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Output abundances" help="" />
-                  <param argument="--reassembly" type="boolean" truevalue="-reassembly" falsevalue="" checked="false" label="Reassembly" help="Reassembly option is still highly experimental. To use this function, you need to feed MaxBin interleaved paired-end fastq or fasta file." />
-              </when>
-              <when value="abdc">
-                  <param name="abund" type="data" format="tabular" multiple="true" label="Abundance file(s)" help="(-abund/-abund2/...)" />
-              </when>
-          </conditional>
-          <conditional name="adv_cond">
-            <param name="adv_select" type="select" label="Advanced options">
-                <option value="yes">Yes</option>
-                <option value="no" selected="true">No</option>
+        <expand macro="contig"/>
+        <conditional name="assembly">
+            <param name="type" type="select" label="Assembly type used to generate contig(s)">
+                <option value="individual">Assembly of sample(s) one by one (individual assembly)</option>
+                <option value="coassembly">Assembly of different samples together (co-assembly)</option>
             </param>
-            <when value="no"/>
-            <when value="yes">
-                <param argument="-min_contig_length" type="integer" min="0" value="1000" label="minimum contig length" />
-                <param argument="-max_iteration" type="integer" min="0" value="50" label="Maximum Expectation-Maximization algorithm iteration number" />
-                <param argument="-prob_threshold" type="float" min="0" max="1.0" value="0.5" label="Probability threshold for EM final classification" />
-                <param argument="-plotmarker" type="boolean" truevalue="-plotmarker" falsevalue="" checked="false" label="Generate visualization of the marker gene presence numbers" />
-                <param name="output_marker" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Output marker gene presence for bins table" />
-                <param name="output_markers" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Output marker genes for each bin as fasta" />
-                <param name="output_log" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Output log" />
-                <param argument="-markerset" type="select" label="Marker gene set">
-                    <option value="107" selected="true">107 marker genes present in >95% of bacteria</option>
-                    <option value="40">40 marker gene sets that are universal among bacteria and archaea</option>
-                </param>
+            <when value="individual">
+                <conditional name="inputs">
+                    <expand macro="input_type"/>
+                    <when value="reads">
+                        <param argument="-reads" type="data" format="fasta,fastq" label="Reads file"/>
+                        <expand macro="reads_extra_params"/>
+                    </when>
+                    <when value="abund">
+                        <param argument="-abund" type="data" format="tabular" label="Abundance file"/>
+                    </when>
+                </conditional>
+            </when>
+            <when value="coassembly">
+                <conditional name="inputs">
+                    <expand macro="input_type"/>
+                    <when value="reads">
+                        <param argument="-reads" type="data" multiple="true" format="fasta,fastq" label="Reads file(s)"/>
+                        <expand macro="reads_extra_params"/>
+                    </when>
+                    <when value="abund">
+                        <param argument="-abund" type="data" format="tabular" multiple="true" label="Abundance file(s)"/>
+                    </when>
+                </conditional>
             </when>
         </conditional>
+        <section name="adv" title="Advanced options">
+            <param argument="-min_contig_length" type="integer" min="0" value="1000" label="minimum contig length" />
+            <param argument="-max_iteration" type="integer" min="0" value="50" label="Maximum Expectation-Maximization algorithm iteration number" />
+            <param argument="-prob_threshold" type="float" min="0" max="1.0" value="0.5" label="Probability threshold for EM final classification" />
+        </section>
+        <section name="output" title="Outputs">
+            <param argument="-plotmarker" type="boolean" truevalue="-plotmarker" falsevalue="" checked="false" label="Generate visualization of the marker gene presence numbers" />
+            <param name="marker" type="boolean" checked="false" label="Output marker gene presence for bins table" />
+            <param name="markers" type="boolean" checked="false" label="Output marker genes for each bin as fasta" />
+            <param name="log" type="boolean" checked="false" label="Output log" />
+            <param argument="-markerset" type="select" label="Marker gene set">
+                <option value="107" selected="true">107 marker genes present in >95% of bacteria</option>
+                <option value="40">40 marker gene sets that are universal among bacteria and archaea</option>
+            </param>
+        </section>
     </inputs>
     <outputs>
         <!-- default outputs -->
-        <collection name="bins" type="list" label="${tool.name} on ${on_string} (bins)">
+        <collection name="bins" type="list" label="${tool.name} on ${on_string}: Bins">
             <discover_datasets pattern="out.(?P&lt;designation&gt;[0-9]+).fasta" format="fasta" visible="false" />
         </collection>
-        <data name="noclass" format="fasta" label="${tool.name} on ${on_string} (unclassified sequences)" from_work_dir="out.noclass"/>
-        <data name="toshort" format="fasta" label="${tool.name} on ${on_string} (to short sequences)" from_work_dir="out.tooshort"/>
-        <data name="summary" format="tabular" label="${tool.name} on ${on_string} (summary)" from_work_dir="out.summary"/>
-
+        <data name="noclass" format="fasta" label="${tool.name} on ${on_string}: Unclassified sequences" from_work_dir="out.noclass"/>
+        <data name="toshort" format="fasta" label="${tool.name} on ${on_string}: Too short sequences" from_work_dir="out.tooshort"/>
+        <data name="summary" format="tabular" label="${tool.name} on ${on_string}: Summary" from_work_dir="out.summary"/>
         <!-- optional outputs -->
-        <data name="log" format="txt" label="${tool.name} on ${on_string} (log)" from_work_dir="out.log">
-            <filter>adv_cond['adv_select']=='yes' and adv_cond['output_log']</filter>
+        <data name="log" format="txt" label="${tool.name} on ${on_string}: Log" from_work_dir="out.log">
+            <filter>output['log']</filter>
         </data>
-        <data name="marker" format="tabular" label="${tool.name} on ${on_string} (marker gene presence)" from_work_dir="out.marker">
-            <filter>adv_cond['adv_select']=='yes' and adv_cond['output_marker']</filter>
+        <data name="marker" format="tabular" label="${tool.name} on ${on_string}: Marker gene presence" from_work_dir="out.marker">
+            <filter>output['marker']</filter>
         </data>
-        <data name="abundout" format="tabular" label="${tool.name} on ${on_string} (abundances)" from_work_dir="out.abund1">
-            <filter>intype_cond['intype_select']=='rds' and intype_cond['output_abundances']</filter>
+        <data name="abundout" format="tabular" label="${tool.name} on ${on_string}: Abundances" from_work_dir="out.abund1">
+            <filter>assembly['inputs']['type']=='reads' and assembly['inputs']['output_abundances']</filter>
         </data>
-        <data name="plot" format="pdf" label="${tool.name} on ${on_string} (marker gene presence plot)" from_work_dir="out.marker.pdf">
-            <filter>adv_cond['adv_select']=='yes' and adv_cond['plotmarker']</filter>
+        <data name="plot" format="pdf" label="${tool.name} on ${on_string}: Marker gene presence plot" from_work_dir="out.marker.pdf">
+            <filter>output['plotmarker']</filter>
         </data>
-        <collection name="markers" type="list" label="${tool.name} on ${on_string} (markers prediced for bins)">
+        <collection name="markers" type="list" label="${tool.name} on ${on_string}: Markers prediced for bins">
             <discover_datasets pattern="out.(?P&lt;designation&gt;[0-9]+).marker.fasta" format="fasta" visible="false" />
-            <filter>adv_cond['adv_select']=='yes' and adv_cond['output_markers']</filter>
+            <filter>output['markers']</filter>
         </collection>
-
         <!-- additional output in case of reassembly -->
-        <collection name="reassembly_bins" type="list" label="${tool.name} on ${on_string} (reassembly bins)">
+        <collection name="reassembly_bins" type="list" label="${tool.name} on ${on_string}: Reassembly bins">
             <discover_datasets directory="out.reassem" pattern="out.(?P&lt;designation&gt;[0-9]+).fasta" format="fasta" visible="false" />
-            <filter>intype_cond['intype_select']=='rds' and intype_cond['reassembly']</filter>
+            <filter>assembly['inputs']['type']=='reads' and assembly['inputs']['reassembly']</filter>
         </collection>
-        <collection name="reassembly_reads" type="list" label="${tool.name} on ${on_string} (reassembly reads)">
+        <collection name="reassembly_reads" type="list" label="${tool.name} on ${on_string}: Reassembly reads">
             <discover_datasets directory="out.reassem" pattern="out.reads.(?P&lt;designation&gt;[0-9]+)" format="fasta" visible="false" />
-            <filter>intype_cond['intype_select']=='rds' and intype_cond['reassembly']</filter>
+            <filter>assembly['inputs']['type']=='reads' and assembly['inputs']['reassembly']</filter>
         </collection>
-        <data name="reassembly_noclass" format="fasta" label="${tool.name} on ${on_string} (reassembly unclassified sequences)" from_work_dir="out.reassem/out.reads.noclass">
-            <filter>intype_cond['intype_select']=='rds' and intype_cond['reassembly']</filter>
+        <data name="reassembly_noclass" format="fasta" label="${tool.name} on ${on_string}: Reassembly unclassified sequences" from_work_dir="out.reassem/out.reads.noclass">
+            <filter>assembly['inputs']['type']=='reads' and assembly['inputs']['reassembly']</filter>
         </data>
-        <data name="reassembly_n50" format="txt" label="${tool.name} on ${on_string} (reassembly N50)" from_work_dir="out.reassem/N50.txt">
-            <filter>intype_cond['intype_select']=='rds' and intype_cond['reassembly']</filter>
+        <data name="reassembly_n50" format="txt" label="${tool.name} on ${on_string}: Reassembly N50" from_work_dir="out.reassem/N50.txt">
+            <filter>assembly['inputs']['type']=='reads' and assembly['inputs']['reassembly']</filter>
         </data>
     </outputs>
     <tests>
         <!-- test w contigs and reads as input -->
         <test expect_num_outputs="4">
             <param name="contig" value="Bin_Sample3_contigs.fasta" ftype="fasta" />
-            <conditional name="intype_cond">
-                <param name="intype_select" value="rds"/>
-                <param name="reads" value="interleavedPE_unmapped_Sample3_small.fasta" ftype="fasta"/>
+            <conditional name="assembly">
+                <param name="type" value="individual"/>
+                <conditional name="inputs">
+                    <param name="type" value="reads"/>
+                    <param name="reads" value="interleavedPE_unmapped_Sample3_small.fasta" ftype="fasta"/>
+                    <param name="output_abundances" value="false"/>
+                    <param name="reassembly" value=""/>
+                </conditional>
             </conditional>
-            <conditional name="adv_cond">
-                <param name="adv_select" value="no"/>
-            </conditional>
+            <section name="adv">
+                <param name="min_contig_length" value="1000"/>
+                <param name="max_iteration" value="50"/>
+                <param name="prob_threshold" value="0.5"/>
+            </section>
+            <section name="output">
+                <param name="plotmarker" value=""/>
+                <param name="marker" value="false"/>
+                <param name="markers" value="false" />
+                <param name="log" value="false"/>
+                <param name="markerset" value="107"/>
+            </section>
             <output_collection name="bins" type="list" count="2">
                 <element name="001" file="1/out.001.fasta" ftype="fasta"/>
                 <element name="002" file="1/out.002.fasta" ftype="fasta"/>
@@ -160,29 +205,49 @@
             <output name="noclass" file="1/out.noclass" ftype="fasta" />
             <output name="toshort" file="1/out.tooshort" ftype="fasta" />
         </test>
-        <!-- test w contigs and reads as input test for optional outputs -->
+        <!-- test w co-assembled contigs and multiple reads and optional outputs -->
         <test expect_num_outputs="9">
             <param name="contig" value="Bin_Sample3_contigs.fasta" ftype="fasta" />
-            <conditional name="intype_cond">
-                <param name="intype_select" value="rds"/>
-                <param name="reads" value="interleavedPE_unmapped_Sample3_small.fasta" ftype="fasta"/>
-                <param name="output_abundances" value="true" />
+            <conditional name="assembly">
+                <param name="type" value="coassembly"/>
+                <conditional name="inputs">
+                    <param name="type" value="reads"/>
+                    <param name="reads" value="interleavedPE_unmapped_Sample3_small.fasta,interleavedPE_unmapped_Sample3_small.fasta" ftype="fasta"/>
+                    <param name="output_abundances" value="true"/>
+                    <param name="reassembly" value=""/>
+                </conditional>
             </conditional>
-            <conditional name="adv_cond">
-                <param name="adv_select" value="yes"/>
-                <param name="plotmarker" value="true" />
-                <param name="output_marker" value="true" />
-                <param name="output_markers" value="true" />
-                <param name="output_log" value="true" />
-            </conditional>
+            <section name="adv">
+                <param name="min_contig_length" value="1000"/>
+                <param name="max_iteration" value="50"/>
+                <param name="prob_threshold" value="0.5"/>
+            </section>
+            <section name="output">
+                <param name="plotmarker" value="true"/>
+                <param name="marker" value="true"/>
+                <param name="markers" value="true" />
+                <param name="log" value="true"/>
+                <param name="markerset" value="107"/>
+            </section>
             <output_collection name="bins" type="list" count="2">
                 <element name="001" file="1/out.001.fasta" ftype="fasta"/>
                 <element name="002" file="1/out.002.fasta" ftype="fasta"/>
             </output_collection>
-            <output name="summary" file="1/out.summary" ftype="tabular" />
+            <output name="summary" ftype="tabular">
+                <assert_contents>
+                    <has_text text="Completeness"/>
+                    <has_text text="out.001.fasta"/>
+                </assert_contents>
+            </output>
             <output name="noclass" file="1/out.noclass" ftype="fasta" />
             <output name="toshort" file="1/out.tooshort" ftype="fasta" />
-            <output name="log" file="1/out.log" ftype="txt" compare="diff" lines_diff="21" />
+            <output name="log" ftype="txt" >
+                <assert_contents>
+                    <has_text text="Input contig"/>
+                    <has_text text="Elapsed time"/>
+                    <has_text text="Yielded 2 bins for contig (scaffold) file"/>
+                </assert_contents>
+            </output>
             <output name="abundout" file="1/out.abund1" ftype="tabular" />
             <output name="marker" file="1/out.marker" ftype="tabular" />
             <output name="plot" file="1/out.marker.pdf" ftype="pdf" compare="sim_size" />
@@ -193,18 +258,25 @@
         <!--test w contigs and abundances as input + advanced options -->
         <test expect_num_outputs="5">
             <param name="contig" value="Bin_Sample3_contigs.fasta" ftype="fasta" />
-            <conditional name="intype_cond">
-                <param name="intype_select" value="abdc"/>
-                <param name="abund" value="abundances.tsv" ftype="tabular"/>
+            <conditional name="assembly">
+                <param name="type" value="individual"/>
+                <conditional name="inputs">
+                    <param name="type" value="abund"/>
+                    <param name="abund" value="abundances.tsv" ftype="tabular"/>
+                </conditional>
             </conditional>
-            <conditional name="adv_cond">
-                <param name="adv_select" value="yes"/>
+            <section name="adv">
                 <param name="min_contig_length" value="500"/>
                 <param name="max_iteration" value="10"/>
                 <param name="prob_threshold" value="0.95"/>
+            </section>
+            <section name="output">
                 <param name="plotmarker" value="-plotmarker"/>
+                <param name="marker" value="false"/>
+                <param name="markers" value="false" />
+                <param name="log" value="false"/>
                 <param name="markerset" value="107"/>
-            </conditional>
+            </section>
             <output_collection name="bins" type="list" count="2">
                 <element name="001" file="2/out.001.fasta" ftype="fasta"/>
                 <element name="002" file="2/out.002.fasta" ftype="fasta"/>
@@ -217,14 +289,27 @@
         <!-- test w contigs and reads as input + reassembly-->
         <test expect_num_outputs="8">
             <param name="contig" value="Bin_Sample3_contigs.fasta" ftype="fasta" />
-            <conditional name="intype_cond">
-                <param name="intype_select" value="rds"/>
-                <param name="reads" value="interleavedPE_unmapped_Sample3_small.fasta" ftype="fasta"/>
-                <param name="reassembly" value="-reassembly"/>
+            <conditional name="assembly">
+                <param name="type" value="individual"/>
+                <conditional name="inputs">
+                    <param name="type" value="reads"/>
+                    <param name="reads" value="interleavedPE_unmapped_Sample3_small.fasta" ftype="fasta"/>
+                    <param name="output_abundances" value="false"/>
+                    <param name="reassembly" value="-reassembly"/>
+                </conditional>
             </conditional>
-            <conditional name="adv_cond">
-                <param name="adv_select" value="no"/>
-            </conditional>
+            <section name="adv">
+                <param name="min_contig_length" value="1000"/>
+                <param name="max_iteration" value="50"/>
+                <param name="prob_threshold" value="0.5"/>
+            </section>
+            <section name="output">
+                <param name="plotmarker" value=""/>
+                <param name="marker" value="false"/>
+                <param name="markers" value="false" />
+                <param name="log" value="false"/>
+                <param name="markerset" value="107"/>
+            </section>
             <output_collection name="bins" type="list" count="2">
                 <element name="001" file="3/out.001.fasta" ftype="fasta"/>
                 <element name="002" file="3/out.002.fasta" ftype="fasta"/>
@@ -233,15 +318,31 @@
             <output name="noclass" file="3/out.noclass" ftype="fasta" />
             <output name="toshort" file="3/out.tooshort" ftype="fasta" />
             <output_collection name="reassembly_bins" type="list" count="2">
-                <element name="001" file="3/out.reassem/out.001.fasta" ftype="fasta"/>
-                <element name="002" file="3/out.reassem/out.002.fasta" ftype="fasta"/>
+                <element name="001" ftype="fasta">
+                    <assert_contents>
+                        <has_text text=">scaffold_0"/>
+                        <has_text text=">scaffold_523"/>
+                    </assert_contents>
+                </element>
+                <element name="002" ftype="fasta">
+                    <assert_contents>
+                        <has_text text=">scaffold_0"/>
+                        <has_text text=">scaffold_523"/>
+                    </assert_contents>
+                </element>
             </output_collection>
             <output_collection name="reassembly_reads" type="list" count="2">
                 <element name="001" file="3/out.reassem/out.reads.001" ftype="fasta"/>
                 <element name="002" file="3/out.reassem/out.reads.002" ftype="fasta"/>
             </output_collection>
             <output name="reassembly_noclass" file="3/out.reassem/out.reads.noclass" ftype="fasta" />
-            <output name="reassembly_n50" file="3/out.reassem/N50.txt" ftype="txt" />
+            <output name="reassembly_n50" ftype="txt">
+                <assert_contents>
+                    <has_text text="N50 before reassem"/>
+                    <has_text text="out.002.fasta"/>
+                    <has_text text="2878"/>
+                </assert_contents>
+            </output>
         </test>
     </tests>
     <help><![CDATA[