diff plink.xml @ 9:272aca44b3dd draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"

--- a/plink.xml	Thu Dec 02 16:20:30 2021 +0000
+++ b/plink.xml	Sun Dec 19 15:53:35 2021 +0000
@@ -1,7 +1,7 @@
 <tool id='plink' name='plink' version='@TOOL_VERSION@+galaxy@VERSION_SUFFIX@'>
     <macros>
-        <token name='@TOOL_VERSION@'>1.9.b618</token>
-        <token name='@VERSION_SUFFIX@'>3</token>
+        <token name='@TOOL_VERSION@'>1.90b6.21</token>
+        <token name='@VERSION_SUFFIX@'>0</token>
         <xml name='template_sanitizer'>
             <sanitizer>
                 <valid initial='default'>
@@ -37,12 +37,19 @@
                 </valid>
             </sanitizer>
         </xml>
+        <xml name="log_out_assert">
+            <output name="plink_log">
+                <assert_contents>
+                    <has_text text="End time:"/>
+                </assert_contents>
+            </output>
+        </xml>
     </macros>
     <xrefs>
         <xref type="bio.tools">plink</xref>
     </xrefs>
     <requirements>
-        <requirement type='package' version='1.90b6.18'>plink</requirement>
+        <requirement type='package' version='@TOOL_VERSION@'>plink</requirement>
     </requirements>
     <command detect_errors='exit_code'><![CDATA[
 
@@ -55,17 +62,17 @@
     #if $functions.func == 'data_manage':
         #if $functions.bmerge.set == 'Yes':
             && mkdir bmerge_files
-            && ln -s '$functions.bmerge.bed' bmerge_files/bmerge_input.bed
-            && ln -s '$functions.bmerge.bim' bmerge_files/bmerge_input.bim
-            && ln -s '$functions.bmerge.fam' bmerge_files/bmerge_input.fam
+            && ln -s '$functions.bmerge.bed.extra_files_path'/RgeneticsData.bed bmerge_files/bmerge_input.bed
+            && ln -s '$functions.bmerge.bed.extra_files_path'/RgeneticsData.bim bmerge_files/bmerge_input.bim
+            && ln -s '$functions.bmerge.bed.extra_files_path'/RgeneticsData.fam bmerge_files/bmerge_input.fam
         #end if
     #end if
 
 
     #if $inputs.inputs.filetype == 'bfile':
-        && ln -s '$inputs.inputs.bed' plink_input/plink_input.bed
-        && ln -s '$inputs.inputs.bim' plink_input/plink_input.bim
-        && ln -s '$inputs.inputs.fam' plink_input/plink_input.fam
+        && ln -s '$inputs.inputs.bed.extra_files_path'/RgeneticsData.bed plink_input/plink_input.bed
+        && ln -s '$inputs.inputs.bed.extra_files_path'/RgeneticsData.bim plink_input/plink_input.bim
+        && ln -s '$inputs.inputs.bed.extra_files_path'/RgeneticsData.fam plink_input/plink_input.fam
         && plink --bfile plink_input/plink_input
     #elif $inputs.inputs.filetype == 'vcf':
         #if $inputs.inputs.input.is_of_type('bcf'):
@@ -402,6 +409,10 @@
             && find ./assoc_out/. -type f -exec mv {} {}.txt ';'
         #end if
     #end if
+    && mkdir '$plink_out.extra_files_path'
+    && cp plink_output/plink_output.bed '$plink_out.extra_files_path'/RgeneticsData.bed
+    && cp plink_output/plink_output.bim '$plink_out.extra_files_path'/RgeneticsData.bim
+    && cp plink_output/plink_output.fam '$plink_out.extra_files_path'/RgeneticsData.fam
     ]]></command>
     <inputs>
         <section name='inputs' title='Data inputs' expanded='true'>
@@ -412,8 +423,6 @@
                 </param>
                 <when value='bfile'>
                     <param format='pbed' name='bed' type='data' label='plink bed file'/>
-                    <param format='tabular,tsv' name='bim' type='data' label='plink bim file'/>
-                    <param format='txt' name='fam' type='data' label='plink fam file'/>
                 </when>
                 <when value='vcf'>
                     <param name='input' format='vcf,vcf_bgzip,bcf' type='data' label='VCF/BCF Input file'/>
@@ -671,9 +680,7 @@
                     </param>
                     <when value='No'/>
                     <when value='Yes'>
-                        <param format='binary' name='bed' type='data' label='plink bed file'/>
-                        <param format='tabular,tsv' name='bim' type='data' label='plink bim file'/>
-                        <param format='tabular,tsv' name='fam' type='data' label='plink fam file'/>
+                        <param format='pbed' name='bed' type='data' label='plink bed file'/>
                     </when>
                 </conditional>
                 <param name='recode' type='boolean' label='Recode' truevalue='--recode' falsevalue='' checked='false' help='Create a new text fileset, after applying sample/variant filters and other operations'/>
@@ -802,7 +809,6 @@
                         <param name='r2' type='float' label='Unphased Hardcall r^2 Threshold' value='0.2' />
                     </when>
                 </conditional>
-
             </when>
             <when value='stratification'>
                 <param name='read_genome' label='Reusing an IBS/IBD calculation' format='tabular,tsv' type='data' optional='true'/>
@@ -993,38 +999,35 @@
     </inputs>
     <outputs>
         <!--Main-->
-        <collection name='plink_out' type='list' label='Plink main outputs'>
-            <data name='plink_bed' format='pbed' from_work_dir='plink_output/plink_output.bed'/>
-            <data name='plink_bim' format='tabular' from_work_dir='plink_output/plink_output.bim'/>
-            <data name='plink_fam' format='txt' from_work_dir='plink_output/plink_output.fam'/>
-            <data name='plink_log' format='txt' from_work_dir='plink_output/plink_output.log'/>
-        </collection>
+        <data name="plink_out" format="pbed"/>
+
+        <data name="plink_log" format='txt' from_work_dir='plink_output/plink_output.log' label='${tool.name} on ${on_string}: Log'/>
 
         <!--Data Manage-->
-        <data name='plink_ped' format='txt' from_work_dir='plink_output/plink_output.ped' label='${tool.name}: Recode ped'>
+        <data name='plink_ped' format='txt' from_work_dir='plink_output/plink_output.ped' label='${tool.name} on ${on_string}: Recode ped'>
             <filter>functions['func'] == 'data_manage' and functions['recode']</filter>
         </data>
-        <data name='plink_map' format='txt' from_work_dir='plink_output/plink_output.map' label='${tool.name}: Recode map'>
+        <data name='plink_map' format='txt' from_work_dir='plink_output/plink_output.map' label='${tool.name} on ${on_string}: Recode map'>
             <filter>functions['func'] == 'data_manage' and functions['recode']</filter>
         </data>
 
         <!--Stats-->
-        <data name='frequency' format='tabular' from_work_dir='plink_output/plink_output.frq' label='${tool.name}: freq out'>
+        <data name='frequency' format='tabular' from_work_dir='plink_output/plink_output.frq' label='${tool.name} on ${on_string}: freq out'>
             <filter>functions['func'] == 'stats' and functions['freq']</filter>
         </data>
-        <data name='hardy_out' format='tabular' from_work_dir='plink_output/plink_output.hwe' label='${tool.name}: Hardy-Weinberg equilibrium'>
+        <data name='hardy_out' format='tabular' from_work_dir='plink_output/plink_output.hwe' label='${tool.name} on ${on_string}: Hardy-Weinberg equilibrium'>
             <filter>functions['func'] == 'stats' and functions['hardy']</filter>
         </data>
-        <data name='missing_1' format='tabular' from_work_dir='plink_output/plink_output.imiss' label='${tool.name}: imiss'>
+        <data name='missing_1' format='tabular' from_work_dir='plink_output/plink_output.imiss' label='${tool.name} on ${on_string}: imiss'>
             <filter>functions['func'] == 'stats' and functions['missing']</filter>
         </data>
-        <data name='missing_2' format='tabular' from_work_dir='plink_output/plink_output.lmiss' label='${tool.name}: lmiss'>
+        <data name='missing_2' format='tabular' from_work_dir='plink_output/plink_output.lmiss' label='${tool.name} on ${on_string}: lmiss'>
             <filter>functions['func'] == 'stats' and functions['missing']</filter>
         </data>
-        <data name='het' format='tabular' from_work_dir='plink_output/plink_output.het' label='${tool.name}: Het'>
+        <data name='het' format='tabular' from_work_dir='plink_output/plink_output.het' label='${tool.name} on ${on_string}: Het'>
             <filter>functions['func'] == 'stats' and functions['het']</filter>
         </data>
-        <data name='sex_check' format='tabular' from_work_dir='plink_output/plink_output.sexcheck' label='${tool.name}: Sex check'>
+        <data name='sex_check' format='tabular' from_work_dir='plink_output/plink_output.sexcheck' label='${tool.name} on ${on_string}: Sex check'>
             <filter>functions['func'] == 'stats' and functions['sex']['sex_stats']</filter>
         </data>
         
@@ -1081,13 +1084,15 @@
         </data>
     </outputs>
     <tests>
-        <test expect_num_outputs='5'>
+        <test expect_num_outputs='2'>
             <section name='inputs'>
                 <conditional name='inputs'>
                     <param name='filetype' value='bfile'/>
-                    <param name='bed' value='plink.bed'/>
-                    <param name='bim' value='plink.bim'/>
-                    <param name='fam' value='plink.fam'/>
+                    <param name='bed' value='' ftype="pbed">
+                        <composite_data value="plink.bim"/>
+                        <composite_data value="plink.bed"/>
+                        <composite_data value="plink.fam"/>
+                    </param>
                 </conditional>
             </section>
             <conditional name='functions'>
@@ -1133,29 +1138,34 @@
                     <param name='nonfounders' value='--nonfounders'/>
                 </conditional>
             </conditional>
-            <output_collection name='plink_out' type='list'>
-                <element name='plink_bed' file='test1_out.bed' compare='sim_size'/>
-                <element name='plink_bim' file='test1_out.bim'/>
-                <element name='plink_fam' file='test1_out.fam'/>
-            </output_collection>
+            <output name="plink_out">
+                <extra_files type="file" name="RgeneticsData.bed" value="test1_out.bed" compare='sim_size'/>
+                <extra_files type="file" name="RgeneticsData.bim" value="test1_out.bim"/>
+                <extra_files type="file" name="RgeneticsData.fam" value="test1_out.fam"/>
+            </output>
+            <expand macro="log_out_assert"/>
         </test>
 
-        <test expect_num_outputs='7'>
+        <test expect_num_outputs='4'>
             <section name='inputs'>
                 <conditional name='inputs'>
                     <param name='filetype' value='bfile'/>
-                    <param name='bed' value='plink.bed'/>
-                    <param name='bim' value='plink.bim'/>
-                    <param name='fam' value='plink.fam'/>
+                    <param name='bed' value='' ftype="pbed">
+                        <composite_data value="plink.bim"/>
+                        <composite_data value="plink.bed"/>
+                        <composite_data value="plink.fam"/>
+                    </param>
                 </conditional>
             </section>
             <conditional name='functions'>
                 <param name='func' value='data_manage'/>
                 <conditional name='bmerge'>
                     <param name='set' value='Yes'/>
-                    <param name='bed' value='plink_2.bed'/>
-                    <param name='bim' value='plink_2.bim'/>
-                    <param name='fam' value='plink_2.fam'/>
+                    <param name='bed' value='' ftype="pbed">
+                        <composite_data value="plink_2.bim"/>
+                        <composite_data value="plink_2.bed"/>
+                        <composite_data value="plink_2.fam"/>
+                    </param>
                 </conditional>
                 <param name='recode' value='--recode'/>
                 <param name='template' value='@asd#123'/>
@@ -1168,36 +1178,40 @@
                     <param name='skip' value='a'/>
                 </conditional>
             </conditional>
-            <output_collection name='plink_out' type='list'>
-                <element name='plink_bed' file='test2_out.bed' compare='sim_size'/>
-                <element name='plink_bim' file='test2_out.bim'/>
-                <element name='plink_fam' file='test2_out.fam'/>
-            </output_collection>
+            <output name="plink_out">
+                <extra_files type="file" name="RgeneticsData.bed" value="test2_out.bed" compare='sim_size'/>
+                <extra_files type="file" name="RgeneticsData.bim" value="test2_out.bim"/>
+                <extra_files type="file" name="RgeneticsData.fam" value="test2_out.fam"/>
+            </output>
+            <expand macro="log_out_assert"/>
             <output name='plink_ped' file='out.ped'/>
             <output name='plink_map' file='out.map'/>
         </test>
 
-        <test expect_num_outputs='5'>
+        <test expect_num_outputs='2'>
             <section name='inputs'>
                 <conditional name='inputs'>
                     <param name='filetype' value='vcf'/>
                     <param name='input' value='test.vcf'/>
                 </conditional>
             </section>
-            <output_collection name='plink_out' type='list'>
-                <element name='plink_bed' file='vcf_out.bed'/>
-                <element name='plink_bim' file='vcf_out.bim'/>
-                <element name='plink_fam' file='vcf_out.fam'/>
-            </output_collection>
+            <output name="plink_out">
+                <extra_files type="file" name="RgeneticsData.bed" value="vcf_out.bed" compare='sim_size'/>
+                <extra_files type="file" name="RgeneticsData.bim" value="vcf_out.bim"/>
+                <extra_files type="file" name="RgeneticsData.fam" value="vcf_out.fam"/>
+            </output>
+            <expand macro="log_out_assert"/>
         </test>
 
-        <test expect_num_outputs='11'>
+        <test expect_num_outputs='8'>
             <section name='inputs'>
                 <conditional name='inputs'>
                     <param name='filetype' value='bfile'/>
-                    <param name='bed' value='plink.bed'/>
-                    <param name='bim' value='x_plink.bim'/>
-                    <param name='fam' value='plink.fam'/>
+                    <param name='bed' value='' ftype="pbed">
+                        <composite_data value="x_plink.bim"/>
+                        <composite_data value="plink.bed"/>
+                        <composite_data value="plink.fam"/>
+                    </param>
                 </conditional>
             </section>
             <conditional name='functions'>
@@ -1217,12 +1231,12 @@
                     </conditional>
                 </conditional>
             </conditional>
-            <output_collection name='plink_out' type='list'>
-                <element name='plink_bed' file='stats.bed'/>
-                <element name='plink_bim' file='stats.bim'/>
-                <element name='plink_fam' file='stats.fam'/>
-                <element name='plink_fam' file='stats.fam'/>
-            </output_collection>
+            <output name="plink_out">
+                <extra_files type="file" name="RgeneticsData.bed" value="stats.bed" compare='sim_size'/>
+                <extra_files type="file" name="RgeneticsData.bim" value="stats.bim"/>
+                <extra_files type="file" name="RgeneticsData.fam" value="stats.fam"/>
+            </output>
+            <expand macro="log_out_assert"/>
             <output name='frequency' file='out.freq'/>
             <output name='hardy_out' file='out.hardy'/>
             <output name='missing_1' file='out.imiss'/>
@@ -1231,13 +1245,15 @@
             <output name='sex_check' file='out.sexcheck'/>
         </test>
 
-        <test expect_num_outputs='7'>
+        <test expect_num_outputs='4'>
             <section name='inputs'>
                 <conditional name='inputs'>
                     <param name='filetype' value='bfile'/>
-                    <param name='bed' value='plink.bed'/>
-                    <param name='bim' value='plink.bim'/>
-                    <param name='fam' value='plink.fam'/>
+                    <param name='bed' value='' ftype="pbed">
+                        <composite_data value="plink.bim"/>
+                        <composite_data value="plink.bed"/>
+                        <composite_data value="plink.fam"/>
+                    </param>
                 </conditional>
             </section>
             <conditional name='functions'>
@@ -1249,21 +1265,24 @@
                     <param name='r2' value='0.3'/>
                 </conditional>
             </conditional>
-            <output_collection name='plink_out' type='list'>
-                <element name='plink_bed' file='test5_out.bed' compare='sim_size'/>
-                <element name='plink_bim' file='test5_out.bim'/>
-                <element name='plink_fam' file='test5_out.fam'/>
-            </output_collection>
+            <output name="plink_out">
+                <extra_files type="file" name="RgeneticsData.bed" value="test5_out.bed" compare='sim_size'/>
+                <extra_files type="file" name="RgeneticsData.bim" value="test5_out.bim"/>
+                <extra_files type="file" name="RgeneticsData.fam" value="test5_out.fam"/>
+            </output>
+            <expand macro="log_out_assert"/>
             <output name='prune_in' file='plink.prune.in'/>
         </test>
         
-        <test expect_num_outputs='10'>
+        <test expect_num_outputs='7'>
             <section name='inputs'>
                 <conditional name='inputs'>
                     <param name='filetype' value='bfile'/>
-                    <param name='bed' value='plink.bed'/>
-                    <param name='bim' value='plink.bim'/>
-                    <param name='fam' value='plink.fam'/>
+                    <param name='bed' value='' ftype="pbed">
+                        <composite_data value="plink.bim"/>
+                        <composite_data value="plink.bed"/>
+                        <composite_data value="plink.fam"/>
+                    </param>
                 </conditional>
             </section>
             <conditional name='functions'>
@@ -1279,11 +1298,12 @@
                     </conditional>
                 </conditional>
             </conditional>
-            <output_collection name='plink_out' type='list'>
-                <element name='plink_bed' file='test6_out.bed' compare='sim_size'/>
-                <element name='plink_bim' file='test6_out.bim'/>
-                <element name='plink_fam' file='test6_out.fam'/>
-            </output_collection>
+            <output name="plink_out">
+                <extra_files type="file" name="RgeneticsData.bed" value="test6_out.bed" compare='sim_size'/>
+                <extra_files type="file" name="RgeneticsData.bim" value="test6_out.bim"/>
+                <extra_files type="file" name="RgeneticsData.fam" value="test6_out.fam"/>
+            </output>
+            <expand macro="log_out_assert"/>
             <output name='mds' value='plink.mds' compare='sim_size'/>
             <output name='cluster1' value='plink.cluster1' compare='sim_size'/>
             <output name='cluster2' value='plink.cluster2' compare='sim_size'/>
@@ -1291,13 +1311,15 @@
             <output name='eigenvals' value='plink.mds.eigenval' compare='sim_size'/>
         </test>
 
-        <test expect_num_outputs='8'>
+        <test expect_num_outputs='5'>
             <section name='inputs'>
                 <conditional name='inputs'>
                     <param name='filetype' value='bfile'/>
-                    <param name='bed' value='plink.bed'/>
-                    <param name='bim' value='plink.bim'/>
-                    <param name='fam' value='plink.fam'/>
+                    <param name='bed' value='' ftype="pbed">
+                        <composite_data value="plink.bim"/>
+                        <composite_data value="plink.bed"/>
+                        <composite_data value="plink.fam"/>
+                    </param>
                 </conditional>
             </section>
             <conditional name='functions'>
@@ -1328,11 +1350,12 @@
                 </conditional>
                 <param name='lambda' value='1.0'/>
             </conditional>
-            <output_collection name='plink_out' type='list'>
-                <element name='plink_bed' file='out.assoc.bed' compare='sim_size'/>
-                <element name='plink_bim' file='out.assoc.bim'/>
-                <element name='plink_fam' file='out.assoc.fam'/>
-            </output_collection>
+            <output name="plink_out">
+                <extra_files type="file" name="RgeneticsData.bed" value="out.assoc.bed" compare='sim_size'/>
+                <extra_files type="file" name="RgeneticsData.bim" value="out.assoc.bim"/>
+                <extra_files type="file" name="RgeneticsData.fam" value="out.assoc.fam"/>
+            </output>
+            <expand macro="log_out_assert"/>
             <output_collection name='assoc_outfiles'  type='list' count='2'>
                 <element name='plink_output.assoc.fisher.mperm' value='out.assoc.fisher.mperm' compare='sim_size'/>
                 <element name='plink_output.assoc.fisher' value='out.assoc.fisher'/>
@@ -1347,13 +1370,15 @@
             </output_collection>
         </test>
 
-        <test expect_num_outputs='6'>
+        <test expect_num_outputs='3'>
             <section name='inputs'>
                 <conditional name='inputs'>
                     <param name='filetype' value='bfile'/>
-                    <param name='bed' value='plink.bed'/>
-                    <param name='bim' value='plink.bim'/>
-                    <param name='fam' value='plink.fam'/>
+                    <param name='bed' value='' ftype="pbed">
+                        <composite_data value="plink.bim"/>
+                        <composite_data value="plink.bed"/>
+                        <composite_data value="plink.fam"/>
+                    </param>
                 </conditional>
             </section>
             <conditional name='functions'>
@@ -1365,6 +1390,7 @@
                     <param name='modifiers' value='full,unbounded,nudge'/>
                 </conditional>
             </conditional>
+            <expand macro="log_out_assert"/>
             <output name='genome' file='out.genome'/>
         </test>
     </tests>