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changeset 16:41cea2aa2dce draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
author bgruening
date Fri, 20 Oct 2023 22:03:32 +0000
parents 60024a528cbd
children 0ee0c3089254
files hifiasm.xml test-data/maternal.headers.txt test-data/paternal.headers.txt
diffstat 3 files changed, 272 insertions(+), 22 deletions(-) [+]
line wrap: on
line diff
--- a/hifiasm.xml	Fri Oct 13 07:26:01 2023 +0000
+++ b/hifiasm.xml	Fri Oct 20 22:03:32 2023 +0000
@@ -2,7 +2,7 @@
     <description>haplotype-resolved de novo assembler for PacBio Hifi reads</description>
     <macros>
         <token name="@TOOL_VERSION@">0.19.7</token>
-        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@VERSION_SUFFIX@">1</token>
         <token name="@FORMATS@">fasta,fasta.gz,fastq,fastq.gz</token>
         <xml name="reads">
             <param name="reads" type="data" format="@FORMATS@" multiple="true" label="Input reads" />
@@ -50,20 +50,26 @@
             #end for
         #end if
         #if str($mode.mode_selector) == 'trio':
-            #for idx, read in enumerate($mode.hap1_reads):
-                #set $inputfile = 'hap1_input_%d.%s' % ($idx, $read.dataset.extension)
-                ln -s '$read' $inputfile &&
-                $hap1_inputs.append($inputfile)
-            #end for
-            #for idx, read in enumerate($mode.hap2_reads):
-                #set $inputfile = 'hap2_input_%d.%s' % ($idx, $read.dataset.extension)
-                ln -s '$read' $inputfile &&
-                $hap2_inputs.append($inputfile)
-            #end for
-            #set $hap1_filenames = ' '.join($hap1_inputs)
-            #set $hap2_filenames = ' '.join($hap2_inputs)
-            yak count -k$mode.yak_kmer_length -b$filter_bits -t\${GALAXY_SLOTS:-1} -o hap1.yak $hap1_filenames &&
-            yak count -k$mode.yak_kmer_length -b$filter_bits -t\${GALAXY_SLOTS:-1} -o hap2.yak $hap2_filenames &&
+            #if str($mode.trioinput.trio_input_selector) == 'reads':
+                #for idx, read in enumerate($mode.trioinput.hap1_reads):
+                    #set $inputfile = 'hap1_input_%d.%s' % ($idx, $read.dataset.extension)
+                    ln -s '$read' $inputfile &&
+                    $hap1_inputs.append($inputfile)
+                #end for
+                #for idx, read in enumerate($mode.trioinput.hap2_reads):
+                    #set $inputfile = 'hap2_input_%d.%s' % ($idx, $read.dataset.extension)
+                    ln -s '$read' $inputfile &&
+                    $hap2_inputs.append($inputfile)
+                #end for
+                #set $hap1_filenames = ' '.join($hap1_inputs)
+                #set $hap2_filenames = ' '.join($hap2_inputs)
+                yak count -k$mode.yak_kmer_length -b$filter_bits -t\${GALAXY_SLOTS:-1} -o hap1.yak $hap1_filenames &&
+                yak count -k$mode.yak_kmer_length -b$filter_bits -t\${GALAXY_SLOTS:-1} -o hap2.yak $hap2_filenames &&
+            #end if
+            #if str($mode.trioinput.trio_input_selector) == 'lists':
+                #set $hap1_filenames = $mode.trioinput.hap1_list
+                #set $hap2_filenames = $mode.trioinput.hap2_list
+            #end if
         #end if
         hifiasm
         -t \${GALAXY_SLOTS:-1}
@@ -99,10 +105,17 @@
             #end if
         #end if
         #if str($mode.mode_selector) == 'trio':
-            -1 hap1.yak
-            -2 hap2.yak
+            #if str($mode.trioinput.trio_input_selector) == 'reads':
+                -1 hap1.yak
+                -2 hap2.yak
+            #end if
+            #if str($mode.trioinput.trio_input_selector) == 'lists':
+                -3 $hap1_filenames
+                -4 $hap2_filenames
+            #end if
             -c $mode.max_kmers
             -d $mode.min_kmers
+            $mode.trio_dual
         #end if
         #if str($purge_options.purge_selector) == 'set':
             -l $purge_options.purge_level
@@ -175,11 +188,24 @@
             </when>
             <when value="trio">
                 <expand macro="reads" />
-                <param name="hap1_reads" type="data" format="fastq,fastq.gz" multiple="true" label="Haplotype 1 reads" />
-                <param name="hap2_reads" type="data" format="fastq,fastq.gz" multiple="true" label="Haplotype 2 reads" />
+                <conditional name="trioinput">
+                    <param name="trio_input_selector" type="select" label="What parental information are you using?">
+                        <option value="reads">Parental reads (FASTQ files, gzipped or otherwise)</option>
+                        <option value="lists">Lists of reads assigned by parent (text files)</option>
+                    </param>
+                    <when value="reads">
+                        <param name="hap1_reads" type="data" format="fastq,fastq.gz" multiple="true" label="Haplotype 1 reads" />
+                        <param name="hap2_reads" type="data" format="fastq,fastq.gz" multiple="true" label="Haplotype 2 reads" />
+                    </when>
+                    <when value="lists">
+                        <param name="hap1_list" type="data" format="txt,tabular" label="Haplotype 1 read list" />
+                        <param name="hap2_list" type="data" format="txt,tabular" label="Haplotype 2 read list" />
+                    </when>
+                </conditional>
                 <param name="max_kmers" argument="-c" type="integer" value="2" label="Lower bound of the binned k-mer's frequency" />
                 <param name="min_kmers" argument="-d" type="integer" value="5" label="Upper bound of the binned k-mer's frequency" />
                 <param name="yak_kmer_length" type="integer" min="0" max="64" value="31" label="Yak counter k-mer length" />
+                <param name="trio_dual" argument="--trio-dual" type="boolean" truevalue="--trio-dual" falsevalue="" label="Utilize homology information to correct trio-phasing errors" />
             </when>
         </conditional>
         <param name="filter_bits" argument="-f" type="integer" min="0" value="37" label="Bits for bloom filter" help="A value of 0 disables the bloom filter" />       
@@ -428,9 +454,12 @@
             <param name="filter_bits" value="0"/>
             <conditional name="mode">
                 <param name="mode_selector" value="trio"/>
-                <param name="reads" value="child.fasta.gz"/>
-                <param name="hap1_reads" value="paternal.fasta.gz"/>
-                <param name="hap2_reads" value="maternal.fasta.gz"/>
+                <param name="trio_input_selector" value="reads"/>
+                <conditional name="trioinput">
+                    <param name="reads" value="child.fasta.gz"/>
+                    <param name="hap1_reads" value="paternal.fasta.gz"/>
+                    <param name="hap2_reads" value="maternal.fasta.gz"/>
+                </conditional>
                 <param name="max_kmers" value="2"/>
                 <param name="min_kmers" value="5"/>
             </conditional>
@@ -556,6 +585,27 @@
             <param name="bins_out" value="yes" />
             <output_collection name="bin_files" type="list" count="3" />
         </test>
+        <!-- TEST 15: Test trio LIST mode -->
+        <test expect_num_outputs="6">
+            <param name="filter_bits" value="0"/>
+            <param name="log_out" value="yes"/>
+            <conditional name="mode">
+                <param name="mode_selector" value="trio"/>
+                <param name="reads" value="child.fasta.gz"/>
+                <conditional name="trioinput">
+                    <param name="trio_input_selector" value="lists"/>
+                    <param name="hap1_list" value="maternal.headers.txt"/>
+                    <param name="hap2_list" value="paternal.headers.txt"/>
+                </conditional>
+                <param name="max_kmers" value="2"/>
+                <param name="min_kmers" value="5"/>
+            </conditional>
+            <output name="log_file" ftype="txt">
+                <assert_contents>
+                    <has_text text="flagged 100 reads, out of 100 lines in file"/>
+                </assert_contents>
+            </output>
+        </test>
     </tests>
     <help><![CDATA[
 .. class:: infomark
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/maternal.headers.txt	Fri Oct 20 22:03:32 2023 +0000
@@ -0,0 +1,100 @@
+K12_1
+K12_3
+K12_5
+K12_7
+K12_9
+K12_11
+K12_13
+K12_15
+K12_17
+K12_19
+K12_21
+K12_23
+K12_25
+K12_27
+K12_29
+K12_31
+K12_33
+K12_35
+K12_37
+K12_39
+K12_41
+K12_43
+K12_45
+K12_47
+K12_49
+K12_51
+K12_53
+K12_55
+K12_57
+K12_59
+K12_61
+K12_63
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+K12_73
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+K12_79
+K12_81
+K12_83
+K12_85
+K12_87
+K12_89
+K12_91
+K12_93
+K12_95
+K12_97
+K12_99
+K12_101
+K12_103
+K12_105
+K12_107
+K12_109
+K12_111
+K12_113
+K12_115
+K12_117
+K12_119
+K12_121
+K12_123
+K12_125
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+K12_129
+K12_131
+K12_133
+K12_135
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+K12_139
+K12_141
+K12_143
+K12_145
+K12_147
+K12_149
+K12_151
+K12_153
+K12_155
+K12_157
+K12_159
+K12_161
+K12_163
+K12_165
+K12_167
+K12_169
+K12_171
+K12_173
+K12_175
+K12_177
+K12_179
+K12_181
+K12_183
+K12_185
+K12_187
+K12_189
+K12_191
+K12_193
+K12_195
+K12_197
+K12_199
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/paternal.headers.txt	Fri Oct 20 22:03:32 2023 +0000
@@ -0,0 +1,100 @@
+K12_699
+K12_701
+K12_703
+K12_705
+K12_707
+K12_709
+K12_711
+K12_713
+K12_715
+K12_717
+K12_719
+K12_721
+K12_723
+K12_725
+K12_727
+K12_729
+K12_731
+K12_733
+K12_735
+K12_737
+K12_739
+K12_741
+K12_743
+K12_745
+K12_747
+K12_749
+K12_751
+K12_753
+K12_755
+K12_757
+K12_759
+K12_761
+K12_763
+K12_765
+K12_767
+K12_769
+K12_771
+K12_773
+K12_775
+K12_777
+K12_779
+K12_781
+K12_783
+K12_785
+K12_787
+K12_789
+K12_791
+K12_793
+K12_795
+K12_797
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+K12_803
+K12_805
+K12_807
+K12_809
+K12_811
+K12_813
+K12_815
+K12_817
+K12_819
+K12_821
+K12_823
+K12_825
+K12_827
+K12_829
+K12_831
+K12_833
+K12_835
+K12_837
+K12_839
+K12_841
+K12_843
+K12_845
+K12_847
+K12_849
+K12_851
+K12_853
+K12_855
+K12_857
+K12_859
+K12_861
+K12_863
+K12_865
+K12_867
+K12_869
+K12_871
+K12_873
+K12_875
+K12_877
+K12_879
+K12_881
+K12_883
+K12_885
+K12_887
+K12_889
+K12_891
+K12_893
+K12_895
+K12_897