# HG changeset patch
# User richard-burhans
# Date 1722286423 0
# Node ID f9e91add973cfbec12102ea626083e1e1b05f037
# Parent  ae2cd39594ebe919d165476d1a7cadbf048b63db
planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign commit eb6ee047d39760f2596b6e343e2dc3898fafc5cd

diff -r ae2cd39594eb -r f9e91add973c gapped_extension_options.xml
--- a/gapped_extension_options.xml	Sat Jul 13 16:51:52 2024 +0000
+++ b/gapped_extension_options.xml	Mon Jul 29 20:53:43 2024 +0000
@@ -1,7 +1,6 @@
 <macros>
     <xml name="gapped_extension_options">
         <section name="gapped_extension_options" expanded="false" title="Gapped Extension Options">
-            <param argument="--nogapped" type="boolean" checked="false" label="Don't perform gapped extension stage"/>
             <param argument="--ydrop" type="integer" value="9430" label="Y-drop value for gapped extension"/>
             <param argument="--gappedthresh" type="integer" value="" optional="true" label="Score threshold for gapped alignments"/>
             <param argument="--notrivial" type="boolean" checked="false" label="Don't output a trivial self-alignment block if the target and query sequences are identical"/>
diff -r ae2cd39594eb -r f9e91add973c output_options.xml
--- a/output_options.xml	Sat Jul 13 16:51:52 2024 +0000
+++ b/output_options.xml	Mon Jul 29 20:53:43 2024 +0000
@@ -1,8 +1,95 @@
 <macros>
     <xml name="output_options">
         <section name="output_options" expanded="false" title="Output Options">
-            <yield/>
-            <param argument="--markend" type="boolean" value="false" label="Write a marker line just before completion"/>
+            <conditional name="format">
+                <param name="format_selector" type="select" display="radio" label="Specify the output format">
+                    <option value="bam">BAM --format=sam)</option>
+                    <option value="general_def">General default (--format=general)</option>
+                    <option value="general_full">Customized general (--format=general[:fields])</option>
+                    <option value="maf" selected="true">MAF (--format=maf)</option>
+                    <option value="blastn">blastn (--format=BLASTN)</option>
+                    <option value="differences">Differences (--format=differences)</option>
+                </param>
+                <when value="bam">
+                    <param name="bam_options" type="select" display="radio" argument="--format=sam, --format=softsam" label="Select a BAM flavor to output" help="Lastz actually outputs SAM data but Galaxy converts it into BAM to save space. For alignments that don't reach the end of a query, ‑‑format=sam uses 'hard clipping', while ‑‑format=softsam uses 'soft clipping'. See the section on 'clipped alignment' in the SAM specification for an explanation of what this means. The options ‑‑format=sam- and ‑‑format=softsam- suppress the SAM header lines. This makes them suitable for concatenating output from multiple runs. If you need to specify readgroup information: use AddOrEplaceReadGroups from Picard package">
+                        <option value="sam">BAM</option>
+                        <option value="softsam">soft-clipped BAM</option>
+                        <option value="sam-">BAM without header</option>
+                        <option value="softsam-">soft-clipped BAM without header</option>
+                    </param>
+                </when>
+                <when value="general_def">
+                    <!-- Do nothing -->
+                </when>
+                <when value="general_full">
+                    <param name="fields" type="select" display="checkboxes" multiple="true" label="Select which fields to include" argument="--format=general-[:fields]">
+                        <option value="score" selected="true">score: Score of the alignment block</option>
+                        <option value="name1" selected="true">name1: Name of the target sequence</option>
+                        <option value="number1">number1: Number of the target sequence within the target file</option>
+                        <option value="strand1" selected="true">strand1: Target sequence strand </option>
+                        <option value="size1" selected="true">size1: Size of the entire target sequence</option>
+                        <option value="start1">start1: Starting position of the alignment block in the target, origin-one</option>
+                        <option value="zstart1" selected="true">zstart1: Starting position of the alignment block in the target, origin-zero</option>
+                        <option value="end1" selected="true">end1: Ending position of the alignment block in the target</option>
+                        <option value="length1">length1: Length of the alignment block in the target (excluding gaps)</option>
+                        <option value="text1">text1: Aligned characters in the target, including gap characters</option>
+                        <option value="qalign1">qalign1: The target quality sequence (if there is one) correpsonding to aligned characters</option>
+                        <option value="nucs1">nucs1: The entire target sequence</option>
+                        <option value="name2" selected="true">name2: Name of the query sequence</option>
+                        <option value="number2">number2: Number of the query sequence within the query file</option>
+                        <option value="strand2" selected="true">strand2: Query sequence strand</option>
+                        <option value="size2" selected="true">size2: Size of the entire query sequence</option>
+                        <option value="start2">start2: Starting position of the alignment block in the query, origin-one</option>
+                        <option value="zstart2" selected="true">zstart2: Starting position of the alignment block in the query, origin-one</option>
+                        <option value="end2" selected="true">end2: Ending position of the alignment block in the query</option>
+                        <option value="length2">length2: Length of the alignment block in the query (excluding gaps)</option>
+                        <option value="text2">text2: Aligned characters in the query, including gap characters</option>
+                        <option value="qalign2">qalign2: The query quality sequence (if there is one) correpsonding to aligned characters</option>
+                        <option value="nucs2">nucs2: The entire query sequence</option>
+                        <option value="nmatch">nmatch: Match count</option>
+                        <option value="nmismatch">nmismatch: Mismatch count</option>
+                        <option value="ncolumn">ncolumn: Number of columns in the block. This includes matches, mismatches (substitutions), and gaps</option>
+                        <option value="npair">npair: Number of aligned bases in the block that are matches or mismatches (substitutions)</option>
+                        <option value="ngap">ngap: Gap count, the number of gaps in the block, counting each run of gapped columns as a single gap</option>
+                        <option value="cgap">cgap: Gap column count, the number of gaps in the block, counting each gapped column as a separate gap</option>
+                        <option value="diff">diff: Differences between what would be written for text1 and text2</option>
+                        <option value="cigar">cigar: A CIGAR-like representation of the alignment’s path</option>
+                        <option value="cigarx">cigarx: Same as cigar, but uses a newer syntax that distinguishes matches from substitutions</option>
+                        <option value="identity" selected="true">identity: Fraction of aligned bases in the block that are matches </option>
+                        <option value="idfrac">idfrac: Fraction of aligned bases in the block that are matches </option>
+                        <option value="id%" selected="true">id% Fraction of aligned bases in the block that are matches (as %)</option>
+                        <option value="blastid%">blastid%: Fraction of the alignment block that is matches, as would be reported by NCBI BLAST</option>
+                        <option value="continuity">continuity: Rate of non-gaps (non-indels) in the alignment block</option>
+                        <option value="confrac">confrac: Rate of non-gaps (non-indels) in the alignment block (as fraction)</option>
+                        <option value="con%">con%: Rate of non-gaps (non-indels) in the alignment block (as %)</option>
+                        <option value="coverage" selected="true">coverage: Fraction of the entire input sequence (target or query, whichever is shorter) that is covered by the alignment block</option>
+                        <option value="covfrac">covfrac: Fraction of the entire input sequence (target or query, whichever is shorter) that is covered by the alignment block (as fraction)</option>
+                        <option value="cov%" selected="true">cov%: Fraction of the entire input sequence (target or query, whichever is shorter) that is covered by the alignment block (as %)</option>
+                        <option value="diagonal">diagonal: The diagonal of the start of the alignment block in the DP matrix, expressed as an identifying number start1-start2</option>
+                        <option value="shingle">shingle: A measurement of the shingle overlap between the target and the query</option>
+                        <option value="number">number: The alignment number, counted as alignments are written to output (1-base)</option>
+                        <option value="znumber">znumber: The alignment number, counted as alignments are written to output (0-base)</option>
+                        <sanitizer invalid_char="">
+                            <valid initial="string.letters,string.digits">
+                                <add value="%"/>
+                            </valid>
+                        </sanitizer>
+                    </param>
+                </when>
+                <when value="maf">
+                    <param name="maf_type" type="select" display="radio" argument="--format=maf" label="Select MAF flavor" help="MAF is a multiple alignment format developed at UCSC">
+                        <option value="maf">MAF</option>
+                        <option value="maf+">MAF with additional stats</option>
+                        <option value="maf-" selected="true">MAF without header and comments</option>
+                    </param>
+                </when>
+                <when value="blastn">
+                    <!-- Do nothing -->
+                </when>
+                <when value="differences">
+                    <!-- Do nothing -->
+                </when>
+            </conditional>
         </section>
     </xml>
 </macros>
diff -r ae2cd39594eb -r f9e91add973c segalign.xml
--- a/segalign.xml	Sat Jul 13 16:51:52 2024 +0000
+++ b/segalign.xml	Mon Jul 29 20:53:43 2024 +0000
@@ -8,7 +8,6 @@
         <import>ungapped_extension_options.xml</import>
         <import>gapped_extension_options.xml</import>
         <import>output_options.xml</import>
-        <import>segalign_output_options.xml</import>
         <import>system_options.xml</import>
     </macros>
     <expand macro="edam_ontology"/>
@@ -20,235 +19,135 @@
         <include path="runner.py"/>
     </required_files>
     <command detect_errors="exit_code"><![CDATA[
-##
-## https://www.gnu.org/software/coreutils/manual/html_node/nproc-invocation.html
-##
-## If the OMP_NUM_THREADS or OMP_THREAD_LIMIT environment variables
-## are set, then they will determine the minimum and maximum returned
-## value respectively.
-##
-## This is how you tame nproc(1)
-##
-OMP_THREAD_LIMIT=\${GALAXY_SLOTS:-2}
+## Convert input to 2bit for lastz -------------------------------------
 
-## Mode ----------------------------------------------------------------
+mkdir -p "\$(pwd)/work" &&
+faToTwoBit <(gzip -cdfq '$target') "\$(pwd)/work/ref.2bit" &&
+faToTwoBit <(gzip -cdfq '$query') "\$(pwd)/work/query.2bit" &&
 
-#if str($mode.mode_selector) == "segalign"
-    #if str($mode.gapped_extension_options.nogapped) == "false"
-        mkdir -p "\$(pwd)/work" && 
-        faToTwoBit <(gzip -cdfq '$mode.target') "\$(pwd)/work/ref.2bit" &&
-        faToTwoBit <(gzip -cdfq '$mode.query') "\$(pwd)/work/query.2bit" &&
-    #end if
-    #if str($mode.diagonal_partition_options.diagonal_partition) == "true"
-        #set $segalign_mode = "segalign_diagonal_partition"
-        ## explicitly calling python to bypass a pulsar bug
-        ## https://github.com/galaxyproject/pulsar/issues/341
-        python '$__tool_directory__/runner.py'
-            --output-type tarball
-            --output-file '$segalign_diagonal_partition_output'
-            --diagonal-partition
-            --num-cpu \${GALAXY_SLOTS:-2}
-            --tool_directory '$__tool_directory__'
-    #else
-        #set $segalign_mode = "segalign"
-        python '$__tool_directory__/runner.py'
-            --output-type output
-            --output-file '$segalign_output'
-            --num-cpu \${GALAXY_SLOTS:-2}
-            --tool_directory '$__tool_directory__'
-    #end if
-            '$mode.target'
-            '$mode.query'
-#else if str($mode.mode_selector) == "segalign_repeat_masker"
-    #set $segalign_mode = "segalign_repeat_masker"
-        run_segalign_repeat_masker
-            '$mode.seq_file'
-            --num_cpu \${GALAXY_SLOTS:-2}
-#end if
+## explicitly calling python to bypass a pulsar bug
+## https://github.com/galaxyproject/pulsar/issues/341
+python '$__tool_directory__/runner.py'
+    --output-type tarball
+    --output-file '$segalign_output'
+    --diagonal-partition
+    --num-cpu \${GALAXY_SLOTS:-2}
+    --tool_directory '$__tool_directory__'
+    '$target'
+    '$query'
 
 ## Sequence Options ----------------------------------------------------
 
-            --strand '$mode.sequence_options.strand_selector'
-#if $segalign_mode == "segalign_repeat_masker"
-            --neighbor_proportion '$mode.sequence_options.neighbor_proportion'
-#end if
+    --strand '$sequence_options.strand_selector'
 
 ## Scoring Options -----------------------------------------------------
 
-#set $scoring_pathname = str($mode.scoring_options.scoring)
+#set $scoring_pathname = str($scoring_options.scoring)
 #if $scoring_pathname != "None":
-            --scoring '$scoring_pathname'
+    --scoring '$scoring_pathname'
 #end if
-#if str($mode.scoring_options.ambiguous_selector) != "x"
-    #if str($mode.scoring_options.set_ambiguous_params_selector) == "true"
-        #set $argument_value = ','.join($mode.scoring_options.ambiguous_selector, $mode.scoring_options.ambiguous_reward, $mode.scoring_options.ambiguous_penalty)
-            --ambiguous '$argument_value'
+#if str($scoring_options.ambiguous_selector) != "x"
+    #if str($scoring_options.set_ambiguous_params_selector) == "true"
+        #set $argument_value = ','.join($scoring_options.ambiguous_selector, $scoring_options.ambiguous_reward, $scoring_options.ambiguous_penalty)
+    --ambiguous '$argument_value'
     #else
-            --ambiguous '$ambiguous_selector'
+    --ambiguous '$ambiguous_selector'
     #end if
 #end if
 
 ## Seeding Options -----------------------------------------------------
 
-#if str($mode.seeding_options.seed.seed_selector) == "custom"
-            --seed '$mode.seeding_options.seed.custom_seed'
+#if str($seeding_options.seed.seed_selector) == "custom"
+    --seed '$seeding_options.seed.custom_seed'
 #else
-            --seed '$mode.seeding_options.seed.seed_selector'
+    --seed '$seeding_options.seed.seed_selector'
 #end if
-            --step '$mode.seeding_options.step'
-#if str($mode.seeding_options.notransition) == "true"
-            --notransition
+    --step '$seeding_options.step'
+#if str($seeding_options.notransition) == "true"
+    --notransition
 #end if
 
 ## Ungapped Extension Options ------------------------------------------
 
-            --xdrop '$mode.ungapped_extension_options.xdrop'
-            --hspthresh '$mode.ungapped_extension_options.hspthresh'
-#if str($mode.ungapped_extension_options.noentropy) == "true"
-            --noentropy
+    --xdrop '$ungapped_extension_options.xdrop'
+    --hspthresh '$ungapped_extension_options.hspthresh'
+#if str($ungapped_extension_options.noentropy) == "true"
+    --noentropy
 #end if
 
 ## Gapped Extension Options --------------------------------------------
 
-#if $segalign_mode != "segalign_repeat_masker"
-    #if str($mode.gapped_extension_options.nogapped) == "true"
-            --nogapped
-    #end if
-            --ydrop '$mode.gapped_extension_options.ydrop'
-    #if str($mode.gapped_extension_options.gappedthresh) != ""
-            --gappedthresh '$mode.gapped_extension_options.gappedthresh'
-    #end if
-    #if str($mode.gapped_extension_options.notrivial) == "true"
-            --notrivial
-    #end if
+    --nogapped
+    --ydrop '$gapped_extension_options.ydrop'
+#if str($gapped_extension_options.gappedthresh) != ""
+    --gappedthresh '$gapped_extension_options.gappedthresh'
+#end if
+#if str($gapped_extension_options.notrivial) == "true"
+    --notrivial
 #end if
 
 ## Output Options -----------------------------------------------------
 
-#if $segalign_mode != "segalign_repeat_masker"
-    #if str($mode.output_options.format.format_selector) == "bam"
-            --format '$mode.output_options.format.bam_options'
-    #else if str($mode.output_options.format.format_selector) == "general_def"
-            --format general-
-    #else if str($mode.output_options.format.format_selector) == "general_full"
-            --format 'general-:${mode.output_options.format.fields}'
-    #else if str($mode.output_options.format.format_selector) == "maf"
-            --format '$mode.output_options.format.maf_type'
-    #else if str($mode.output_options.format.format_selector) == "blastn"
-            --format=BLASTN-
-    #else if str($mode.output_options.format.format_selector) == "differences"
-            --format=differences
-    #end if
+#if str($output_options.format.format_selector) == "bam"
+    --format '$output_options.format.bam_options'
+#else if str($output_options.format.format_selector) == "general_def"
+    --format general-
+#else if str($output_options.format.format_selector) == "maf"
+    --format '$output_options.format.maf_type'
+#else if str($output_options.format.format_selector) == "blastn"
+    --format=BLASTN-
+#else if str($output_options.format.format_selector) == "general_full"
+    --format 'general-:${output_options.format.fields}'
+#else if str($output_options.format.format_selector) == "differences"
+    --format=differences
+#end if
     ## todo :: rplot, bam
     ##  --action:target=multiple
     ##  $output_format.rplot
-    ##  .if str( $output_format.out.format ) == "bam":
+    ##  #if str( $output_format.out.format ) == "bam":
     ##      | samtools sort -@\${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" -O bam -o '${output}'
-    ##  .else:
+    ##  #else:
     ##      > '${output}'
-    ##  .end if
-    ##  .if $output_format.rplot:
+    ##  #end if
+    ##  #if $output_format.rplot:
     ##      &&
     ##      Rscript $r_plot > /dev/null 2>&1
-    ##  .end if
-#else if $segalign_mode == "segalign_repeat_masker"
-            --M '$mode.output_options.M'
-            --output '$segalign_repeat_masker_output'
-#end if
-#if str($mode.output_options.markend) == "true"
-            --markend
-#end if
+    ##  #end if
 
 ## System Options -----------------------------------------------------
 
-            --wga_chunk_size '$mode.system_options.wga_chunk_size'
-            --lastz_interval_size '$mode.system_options.lastz_interval_size'
-            --seq_block_size '$mode.system_options.seq_block_size'
-            --num_gpu '$mode.system_options.num_gpu'
-#if str($mode.system_options.debug) == "true"
-            --debug
+    --wga_chunk_size '$system_options.wga_chunk_size'
+    --lastz_interval_size '$system_options.lastz_interval_size'
+    --seq_block_size '$system_options.seq_block_size'
+    --num_gpu '$system_options.num_gpu'
+#if str($system_options.debug) == "true"
+    --debug
 #end if
 
-## -------------------------------------------------------------------
+## Package Output ----------------------------------------------------
 
-#if $segalign_mode == "segalign_diagonal_partition"
-        &&
-        python '$__tool_directory__/package_output.py'
-            --tool_directory '$__tool_directory__'
-#end if
+    && python '$__tool_directory__/package_output.py'
 
     ]]></command>
     <inputs>
-        <conditional name="mode">
-            <param name="mode_selector" type="select" label="Choose the mode">
-                <option value="segalign" selected="true">SegAlign</option>
-                <option value="segalign_repeat_masker">SegAlign repeat masker</option>
-            </param>
-            <when value="segalign">
-                <param name="target" type="data" format="fasta,fasta.gz" label="Target sequence file in FASTA format"/>
-                <param name="query" type="data" format="fasta,fasta.gz" label="Query sequence file in FASTA format"/>
-                <expand macro="sequence_options"/>
-                <expand macro="scoring_options"/>
-                <expand macro="seeding_options"/>
-                <expand macro="ungapped_extension_options"/>
-                <expand macro="gapped_extension_options"/>
-                <expand macro="output_options">
-                    <expand macro="segalign_output_options"/>
-                </expand>
-                <expand macro="system_options"/>
-                <section name="diagonal_partition_options" expanded="false" title="Diagonal Partition Options">
-                    <param argument="--diagonal_partition" type="boolean" value="false" label="Enable diagonal partition optimization"/>
-                </section>
-            </when>
-            <when value="segalign_repeat_masker">
-                <param name="seq_file" type="data" format="fasta,fasta.gz" label="Sequence file in FASTA format"/>
-                <expand macro="sequence_options">
-                    <param argument="--neighbor_proportion" type="float" value="0.2" label="Proportion of neighbouring intervals to align the query interval to"/>
-                </expand>
-                <expand macro="scoring_options"/>
-                <expand macro="seeding_options"/>
-                <expand macro="ungapped_extension_options"/>
-                <expand macro="output_options">
-                    <param argument="--M" type="integer" value="1" max="255" label="report any position that is covered by at least this many alignments; the maximum allowed depth is 255"/>
-                </expand>
-                <expand macro="system_options"/>
-            </when>
-        </conditional>
+        <param name="target" type="data" format="fasta,fasta.gz" label="Target sequence file in FASTA format"/>
+        <param name="query" type="data" format="fasta,fasta.gz" label="Query sequence file in FASTA format"/>
+        <expand macro="sequence_options"/>
+        <expand macro="scoring_options"/>
+        <expand macro="seeding_options"/>
+        <expand macro="ungapped_extension_options"/>
+        <expand macro="gapped_extension_options"/>
+        <expand macro="output_options"/>
+        <expand macro="system_options"/>
     </inputs>
     <outputs>
-        <data name="segalign_output" format="tabular" label="SegAlign on ${on_string}">
-            <change_format>
-                <when input="mode.output_options.format.format_selector" value="bam" format="bam"/>
-                <when input="mode.output_options.format.format_selector" value="maf" format="maf"/>
-                <when input="mode.output_options.format.format_selector" value="differences" format="interval"/>
-            </change_format>
-            <filter>mode['mode_selector'] == 'segalign' and mode['diagonal_partition_options']['diagonal_partition'] is False</filter>
-        </data>
-        <data name="segalign_diagonal_partition_output" format="tgz" from_work_dir="data_package.tgz" label="SegAlign Diagonal Partition on ${on_string}">
-            <filter>mode['mode_selector'] == 'segalign' and mode['diagonal_partition_options']['diagonal_partition'] is True</filter>
-        </data>
-        <data name="segalign_repeat_masker_output" format="tabular" label="SegAlign Repeat Masker on ${on_string}">
-            <filter>mode['mode_selector'] == 'segalign_repeat_masker'</filter>
-        </data>
+        <data name="segalign_output" format="tgz" from_work_dir="data_package.tgz" label="SegAlign on ${on_string}"/>
     </outputs>
     <tests>
         <test expect_num_outputs="1" expect_test_failure="true">
-            <param name="mode_selector" value="segalign"/>
             <param name="target" value="hg38.chr20.chunk.fa.gz" ftype="fasta.gz"/>
             <param name="query" value="mm39.chr2.chunk.fa.gz" ftype="fasta.gz"/>
-            <output name="segalign_output" decompress="true" file="segalign-output.maf.gz" ftype="maf"/>
-        </test>
-        <test expect_num_outputs="1" expect_test_failure="true">
-            <param name="mode_selector" value="segalign_repeat_masker"/>
-            <param name="seq_file" value="hg38.chr20.chunk.fa.gz" ftype="fasta.gz"/>
-            <output name="segalign_repeat_masker_output" decompress="true" file="segalign-repeat-masker-output.tab.gz" ftype="tabular"/>
-        </test>
-        <test expect_num_outputs="1" expect_test_failure="true">
-            <param name="mode_selector" value="segalign"/>
-            <param name="target" value="hg38.chr20.chunk.fa.gz" ftype="fasta.gz"/>
-            <param name="query" value="mm39.chr2.chunk.fa.gz" ftype="fasta.gz"/>
-            <param name="diagonal_partition" value="true"/>
-            <output name="segalign_diagonal_partition_output" ftype="tgz">
+            <output name="segalign_output" ftype="tgz">
                 <assert_contents>
                     <has_archive_member path="galaxy/commands.json"/>
                 </assert_contents>
diff -r ae2cd39594eb -r f9e91add973c segalign_output_options.xml
--- a/segalign_output_options.xml	Sat Jul 13 16:51:52 2024 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,93 +0,0 @@
-<macros>
-    <xml name="segalign_output_options">
-        <conditional name="format">
-            <param name="format_selector" type="select" display="radio" label="Specify the output format">
-                <option value="bam">BAM --format=sam)</option>
-                <option value="general_def">General default (--format=general)</option>
-                <option value="general_full">Customized general (--format=general[:fields])</option>
-                <option value="maf" selected="true">MAF (--format=maf)</option>
-                <option value="blastn">blastn (--format=BLASTN)</option>
-                <option value="differences">Differences (--format=differences)</option>
-            </param>
-            <when value="bam">
-                <param name="bam_options" type="select" display="radio" argument="--format=sam, --format=softsam" label="Select a BAM flavor to output" help="Lastz actually outputs SAM data but Galaxy converts it into BAM to save space. For alignments that don't reach the end of a query, ‑‑format=sam uses 'hard clipping', while ‑‑format=softsam uses 'soft clipping'. See the section on 'clipped alignment' in the SAM specification for an explanation of what this means. The options ‑‑format=sam- and ‑‑format=softsam- suppress the SAM header lines. This makes them suitable for concatenating output from multiple runs. If you need to specify readgroup information: use AddOrEplaceReadGroups from Picard package">
-                    <option value="sam">BAM</option>
-                    <option value="softsam">soft-clipped BAM</option>
-                    <option value="sam-">BAM without header</option>
-                    <option value="softsam-">soft-clipped BAM without header</option>
-                </param>
-            </when>
-            <when value="general_def">
-                <!-- Do nothing -->
-            </when>
-            <when value="general_full">
-                <param name="fields" type="select" display="checkboxes" multiple="true" label="Select which fields to include" argument="--format=general-[:fields]">
-                    <option value="score" selected="true">score: Score of the alignment block</option>
-                    <option value="name1" selected="true">name1: Name of the target sequence</option>
-                    <option value="number1">number1: Number of the target sequence within the target file</option>
-                    <option value="strand1" selected="true">strand1: Target sequence strand </option>
-                    <option value="size1" selected="true">size1: Size of the entire target sequence</option>
-                    <option value="start1">start1: Starting position of the alignment block in the target, origin-one</option>
-                    <option value="zstart1" selected="true">zstart1: Starting position of the alignment block in the target, origin-zero</option>
-                    <option value="end1" selected="true">end1: Ending position of the alignment block in the target</option>
-                    <option value="length1">length1: Length of the alignment block in the target (excluding gaps)</option>
-                    <option value="text1">text1: Aligned characters in the target, including gap characters</option>
-                    <option value="qalign1">qalign1: The target quality sequence (if there is one) correpsonding to aligned characters</option>
-                    <option value="nucs1">nucs1: The entire target sequence</option>
-                    <option value="name2" selected="true">name2: Name of the query sequence</option>
-                    <option value="number2">number2: Number of the query sequence within the query file</option>
-                    <option value="strand2" selected="true">strand2: Query sequence strand</option>
-                    <option value="size2" selected="true">size2: Size of the entire query sequence</option>
-                    <option value="start2">start2: Starting position of the alignment block in the query, origin-one</option>
-                    <option value="zstart2" selected="true">zstart2: Starting position of the alignment block in the query, origin-one</option>
-                    <option value="end2" selected="true">end2: Ending position of the alignment block in the query</option>
-                    <option value="length2">length2: Length of the alignment block in the query (excluding gaps)</option>
-                    <option value="text2">text2: Aligned characters in the query, including gap characters</option>
-                    <option value="qalign2">qalign2: The query quality sequence (if there is one) correpsonding to aligned characters</option>
-                    <option value="nucs2">nucs2: The entire query sequence</option>
-                    <option value="nmatch">nmatch: Match count</option>
-                    <option value="nmismatch">nmismatch: Mismatch count</option>
-                    <option value="ncolumn">ncolumn: Number of columns in the block. This includes matches, mismatches (substitutions), and gaps</option>
-                    <option value="npair">npair: Number of aligned bases in the block that are matches or mismatches (substitutions)</option>
-                    <option value="ngap">ngap: Gap count, the number of gaps in the block, counting each run of gapped columns as a single gap</option>
-                    <option value="cgap">cgap: Gap column count, the number of gaps in the block, counting each gapped column as a separate gap</option>
-                    <option value="diff">diff: Differences between what would be written for text1 and text2</option>
-                    <option value="cigar">cigar: A CIGAR-like representation of the alignment’s path</option>
-                    <option value="cigarx">cigarx: Same as cigar, but uses a newer syntax that distinguishes matches from substitutions</option>
-                    <option value="identity" selected="true">identity: Fraction of aligned bases in the block that are matches </option>
-                    <option value="idfrac">idfrac: Fraction of aligned bases in the block that are matches </option>
-                    <option value="id%" selected="true">id% Fraction of aligned bases in the block that are matches (as %)</option>
-                    <option value="blastid%">blastid%: Fraction of the alignment block that is matches, as would be reported by NCBI BLAST</option>
-                    <option value="continuity">continuity: Rate of non-gaps (non-indels) in the alignment block</option>
-                    <option value="confrac">confrac: Rate of non-gaps (non-indels) in the alignment block (as fraction)</option>
-                    <option value="con%">con%: Rate of non-gaps (non-indels) in the alignment block (as %)</option>
-                    <option value="coverage" selected="true">coverage: Fraction of the entire input sequence (target or query, whichever is shorter) that is covered by the alignment block</option>
-                    <option value="covfrac">covfrac: Fraction of the entire input sequence (target or query, whichever is shorter) that is covered by the alignment block (as fraction)</option>
-                    <option value="cov%" selected="true">cov%: Fraction of the entire input sequence (target or query, whichever is shorter) that is covered by the alignment block (as %)</option>
-                    <option value="diagonal">diagonal: The diagonal of the start of the alignment block in the DP matrix, expressed as an identifying number start1-start2</option>
-                    <option value="shingle">shingle: A measurement of the shingle overlap between the target and the query</option>
-                    <option value="number">number: The alignment number, counted as alignments are written to output (1-base)</option>
-                    <option value="znumber">znumber: The alignment number, counted as alignments are written to output (0-base)</option>
-                    <sanitizer invalid_char="">
-                        <valid initial="string.letters,string.digits">
-                            <add value="%"/>
-                        </valid>
-                    </sanitizer>
-                </param>
-            </when>
-            <when value="maf">
-                <param name="maf_type" type="select" display="radio" argument="--format=maf" label="Select MAF flavor" help="MAF is a multiple alignment format developed at UCSC">
-                    <option value="maf">MAF</option>
-                    <option value="maf+">MAF with additional stats</option>
-                    <option value="maf-" selected="true">MAF without header and comments</option>
-                </param>
-            </when>
-            <when value="blastn">
-                <!-- Do nothing -->
-            </when>
-            <when value="differences">
-                <!-- Do nothing -->
-            </when>
-        </conditional>
-    </xml>
-</macros>
diff -r ae2cd39594eb -r f9e91add973c test-data/segalign-output.maf.gz
Binary file test-data/segalign-output.maf.gz has changed
diff -r ae2cd39594eb -r f9e91add973c test-data/segalign-repeat-masker-output.tab.gz
Binary file test-data/segalign-repeat-masker-output.tab.gz has changed