Repository 'bwa'
hg clone https://toolshed.g2.bx.psu.edu/repos/devteam/bwa

Changeset 18:48f306c57611 (2017-11-24)
Previous changeset 17:d1228ec6233f (2017-11-21) Next changeset 19:dfd8b7f78c37 (2017-12-22)
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
modified:
bwa-mem.xml
bwa.xml
bwa_macros.xml
b
diff -r d1228ec6233f -r 48f306c57611 bwa-mem.xml
--- a/bwa-mem.xml Tue Nov 21 11:24:01 2017 -0500
+++ b/bwa-mem.xml Fri Nov 24 09:55:45 2017 -0500
[
b'@@ -1,63 +1,65 @@\n <?xml version="1.0"?>\n-<tool id="bwa_mem" name="Map with BWA-MEM" version="@VERSION@.0">\n-  <description>- map medium and long reads (&gt; 100 bp) against reference genome</description>\n-  <macros>\n-    <import>read_group_macros.xml</import>\n-    <import>bwa_macros.xml</import>\n-  </macros>\n-  <expand macro="requirements" />\n-  <expand macro="stdio" />\n-  <command>\n+<tool id="bwa_mem" name="Map with BWA-MEM" version="@VERSION@.1">\n+    <description>- map medium and long reads (&gt; 100 bp) against reference genome</description>\n+    <macros>\n+        <import>read_group_macros.xml</import>\n+        <import>bwa_macros.xml</import>\n+    </macros>\n+    <expand macro="requirements"/>\n+    <expand macro="stdio"/>\n+    <command>\n <![CDATA[\n-    @set_reference_fasta_filename@\n+@set_reference_fasta_filename@\n \n-    ## Begin BWA-MEM command line\n+## Begin BWA-MEM command line\n \n-    bwa mem\n-    -t "\\${GALAXY_SLOTS:-1}"\n-    -v 1                                                                                      ## Verbosity is set to 1 (errors only)\n+bwa mem\n+-t "\\${GALAXY_SLOTS:-1}"\n+## Verbosity is set to 1 (errors only)\n+-v 1\n \n-    #if str( $fastq_input.fastq_input_selector ) == "paired_iv":                              ## For interleaved fastq files set -p option\n-      -p\n-      #if str( $fastq_input.iset_stats ):                                                     ## check that insert statistics is used\n-        -I "${fastq_input.iset_stats}"\n-      #end if\n+#if str( $fastq_input.fastq_input_selector ) == "paired_iv":\n+    ## For interleaved fastq files set -p option\n+    -p\n+    ## check that insert statistics is used\n+    #if str( $fastq_input.iset_stats ):\n+      -I \'${fastq_input.iset_stats}\'\n     #end if\n+#end if\n \n-    #if str( $analysis_type.analysis_type_selector ) == "pacbio":\n-      -x pacbio\n-    #elif str( $analysis_type.analysis_type_selector ) == "ont2d":\n-      -x ont2d\n-    #elif str( $analysis_type.analysis_type_selector ) == "intractg":\n-      -x intractg\n-    #elif str( $analysis_type.analysis_type_selector ) == "full":\n-      #if str( $analysis_type.algorithmic_options.algorithmic_options_selector ) == "set":    ## Algorithmic options\n-        -k "${analysis_type.algorithmic_options.k}"\n-        -w "${analysis_type.algorithmic_options.w}"\n-        -d "${analysis_type.algorithmic_options.d}"\n-        -r "${analysis_type.algorithmic_options.r}"\n-        -y "${analysis_type.algorithmic_options.y}"\n-        -c "${analysis_type.algorithmic_options.c}"\n-        -D "${analysis_type.algorithmic_options.D}"\n-        -W "${analysis_type.algorithmic_options.W}"\n-        -m "${analysis_type.algorithmic_options.m}"\n+#if str( $analysis_type.analysis_type_selector ) not in ["illumina", "full"]:\n+    -x \'$analysis_type.analysis_type_selector\'\n+#elif str( $analysis_type.analysis_type_selector ) == "full":\n+    ## Algorithmic options\n+    #if str( $analysis_type.algorithmic_options.algorithmic_options_selector ) == "set":\n+        -k \'${analysis_type.algorithmic_options.k}\'\n+        -w \'${analysis_type.algorithmic_options.w}\'\n+        -d \'${analysis_type.algorithmic_options.d}\'\n+        -r \'${analysis_type.algorithmic_options.r}\'\n+        -y \'${analysis_type.algorithmic_options.y}\'\n+        -c \'${analysis_type.algorithmic_options.c}\'\n+        -D \'${analysis_type.algorithmic_options.D}\'\n+        -W \'${analysis_type.algorithmic_options.W}\'\n+        -m \'${analysis_type.algorithmic_options.m}\'\n         ${analysis_type.algorithmic_options.S}\n         ${analysis_type.algorithmic_options.P}\n         ${analysis_type.algorithmic_options.e}\n-      #end if\n+    #end if\n \n-      #if str( $analysis_type.scoring_options.scoring_options_selector ) == "set":             ## Scoring options\n-        -A "${analysis_type.scoring_options.A}"\n-        -B "${analysis_type.scoring_options.B}"\n-        -O "${analysis_type.scoring_options.O}"\n-        -E "${analysis_type.scoring_options.E}"\n-        -L "${analysis_type.scoring_opti'..b' application in which it alignes single or paired-end data to reference using default parameters. It is equivalent to the following command: bwa mem <reference index> <fastq dataset1> [fastq dataset2]\n+  2. *PacBio mode*: The mode adjusted specifically for mapping of long PacBio subreads. Equivalent to the following command: bwa mem -k17 -W40 -r10 -A1 -B1 -O1 -E1 -L0  <reference index> <PacBio dataset in fastq format>\n   3. *Full list of options*: Allows access to all options through Galaxy interface.\n \n-------\n-\n-**BWA MEM options**\n-\n-Each Galaxy parameter widget corresponds to command line flags listed below:\n-\n-Algorithm options::\n-\n-       -k INT        minimum seed length [19]\n-       -w INT        band width for banded alignment [100]\n-       -d INT        off-diagonal X-dropoff [100]\n-       -r FLOAT      look for internal seeds inside a seed longer than {-k} * FLOAT [1.5]\n-       -y INT        find MEMs longer than {-k} * {-r} with size less than INT [0]\n-       -c INT        skip seeds with more than INT occurrences [500]\n-       -D FLOAT      drop chains shorter than FLOAT fraction of the longest overlapping chain [0.50]\n-       -W INT        discard a chain if seeded bases shorter than INT [0]\n-       -m INT        perform at most INT rounds of mate rescues for each read [50]\n-       -S            skip mate rescue\n-       -P            skip pairing; mate rescue performed unless -S also in use\n-       -e            discard full-length exact matches\n-\n-Scoring options::\n-\n-       -A INT        score for a sequence match, which scales options -TdBOELU unless overridden [1]\n-       -B INT        penalty for a mismatch [4]\n-       -O INT[,INT]  gap open penalties for deletions and insertions [6,6]\n-       -E INT[,INT]  gap extension penalty; a gap of size k cost \'{-O} + {-E}*k\' [1,1]\n-       -L INT[,INT]  penalty for 5\'- and 3\'-end clipping [5,5]\n-       -U INT        penalty for an unpaired read pair [17]\n-\n-Input/output options::\n-\n-       -p            first query file consists of interleaved paired-end sequences\n-       -R STR        read group header line such as \'@RG\\tID:foo\\tSM:bar\' [null]\n-\n-       -v INT        verbose level: 1=error, 2=warning, 3=message, 4+=debugging [3]\n-       -T INT        minimum score to output [30]\n-       -h INT        if there are &lt;INT hits with score &gt;80% of the max score, output all in XA [5]\n-       -a            output all alignments for SE or unpaired PE\n-       -C            append FASTA/FASTQ comment to SAM output\n-       -V            output the reference FASTA header in the XR tag\n-       -Y            use soft clipping for supplementary alignments\n-       -M            mark shorter split hits as secondary\n-\n-       -I FLOAT[,FLOAT[,INT[,INT]]]\n-                     specify the mean, standard deviation (10% of the mean if absent), max\n-                     (4 sigma from the mean if absent) and min of the insert size distribution.\n-                     FR orientation only. [inferred]\n-\n-@dataset_collections@\n-\n @RG@\n \n @info@\n-  </help>\n-  <citations>\n-    <citation type="doi">10.1093/bioinformatics/btp324</citation>\n-    <citation type="doi">10.1093/bioinformatics/btp698</citation>\n-    <citation type="bibtex">@misc{1303.3997,\n-Author = {Heng Li},\n-Title = {Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM},\n-Year = {2013},\n-Eprint = {arXiv:1303.3997},\n-url = {http://arxiv.org/abs/1303.3997},\n-}</citation>\n-  </citations>\n+    ]]></help>\n+    <citations>\n+        <citation type="doi">10.1093/bioinformatics/btp324</citation>\n+        <citation type="doi">10.1093/bioinformatics/btp698</citation>\n+        <citation type="bibtex">@misc{1303.3997,\n+            Author = {Heng Li},\n+            Title = {Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM},\n+            Year = {2013},\n+            Eprint = {arXiv:1303.3997},\n+            url = {http://arxiv.org/abs/1303.3997},\n+            }</citation>\n+    </citations>\n </tool>\n'
b
diff -r d1228ec6233f -r 48f306c57611 bwa.xml
--- a/bwa.xml Tue Nov 21 11:24:01 2017 -0500
+++ b/bwa.xml Fri Nov 24 09:55:45 2017 -0500
[
b'@@ -1,457 +1,412 @@\n <?xml version="1.0"?>\n-<tool id="bwa" name="Map with BWA" version="@VERSION@.2">\n-  <description>- map short reads (&lt; 100 bp) against reference genome</description>\n-  <macros>\n-    <import>read_group_macros.xml</import>\n-    <import>bwa_macros.xml</import>\n-    <token name="@command_options@">\n-    #if str( $analysis_type.analysis_type_selector ) == "full":\n-      -n ${analysis_type.n}\n-      -o ${analysis_type.o}\n-      -e ${analysis_type.e}\n-      -i ${analysis_type.i}\n-      -d ${analysis_type.d}\n-      -l ${analysis_type.l}\n-      -k ${analysis_type.k}\n-      -m ${analysis_type.m}\n-      -M ${analysis_type.M}\n-      -O ${analysis_type.O}\n-      -E ${analysis_type.E}\n-      -R ${analysis_type.R}\n-      -q ${analysis_type.q}\n-\n-      #if str( $analysis_type.B ):\n+<tool id="bwa" name="Map with BWA" version="@VERSION@.3">\n+    <description>- map short reads (&lt; 100 bp) against reference genome</description>\n+    <macros>\n+        <import>read_group_macros.xml</import>\n+        <import>bwa_macros.xml</import>\n+        <token name="@command_options@">\n+#if str( $analysis_type.analysis_type_selector ) == "full":\n+    -n ${analysis_type.n}\n+    -o ${analysis_type.o}\n+    -e ${analysis_type.e}\n+    -i ${analysis_type.i}\n+    -d ${analysis_type.d}\n+    -l ${analysis_type.l}\n+    -k ${analysis_type.k}\n+    -m ${analysis_type.m}\n+    -M ${analysis_type.M}\n+    -O ${analysis_type.O}\n+    -E ${analysis_type.E}\n+    -R ${analysis_type.R}\n+    -q ${analysis_type.q}\n+    #if str( $analysis_type.B ):\n         -B ${analysis_type.B}\n-      #end if\n-\n-      #if str( $analysis_type.L ):\n+    #end if\n+    #if str( $analysis_type.L ):\n         -L ${analysis_type.L}\n-      #end if\n     #end if\n-    </token>\n-    <token name="@read_group_options@">\n-      #if $use_rg:\n-        @set_rg_string@\n-        -r \'$rg_string\'\n-      #end if\n-    </token>\n+#end if\n+        </token>\n+        <token name="@read_group_options@">\n+#if $use_rg:\n+    @set_rg_string@\n+    -r \'$rg_string\'\n+#end if\n+        </token>\n+        <xml name="advanced_pe_options">\n+            <param name="adv_pe_options_selector" type="select" label="Set advanced paired end options?"\n+                   help="Provides additional controls">\n+                <option value="set">Set</option>\n+                <option value="do_not_set" selected="True">Do not set</option>\n+            </param>\n+            <when value="set">\n+                <param name="a" type="integer" value="500"\n+                       label="Maximum insert size for a read pair to be considered being mapped properly."\n+                       help="sampe -a; This option is only used when there are not enough good alignment to infer the distribution of insert sizes; default=500"/>\n+                <param name="o" type="integer" value="100000"\n+                       label="Maximum occurrences of a read for pairing. A read with more occurrences will be treated as a single-end read."\n+                       help="sampe -o; Reducing this parameter helps faster pairing; default=100000"/>\n+                <param name="n" type="integer" value="3"\n+                       label="Maximum number of alignments to output in the XA tag for reads paired properly."\n+                       help="sampe -n; If a read has more than this many hits, the XA tag will not be written; default=3"/>\n+                <param name="N" type="integer" value="10"\n+                       label="Maximum number of alignments to output in the XA tag for disconcordant read pairs (excluding singletons)."\n+                       help="sampe -N; If a read has more than this many hits, the XA tag will not be written; default=10"/>\n+                <param name="c" type="float" value="0.00005" label="Prior of chimeric rate (lower bound)"\n+                       help="sampe -c"/>\n+            </when>\n+            <when value="do_not_set">\n+                <!-- do nothing -->\n+            </when>\n+        </xml>\n+        <xml name="advanced_s'..b'his dropdown have been pre-indexed with bwa index utility\n+     and are ready to be mapped against.\n+  2. **Use a genome from the history and build index** - when selected, Galaxy provides the user with **Select\n+     reference genome sequence** dropdown. This dropdown is populated by all FASTA formatted files listed in your\n+     current history. If your genome of interest is uploaded into history it will be shown there. Selecting a genome\n+     from this dropdown will cause Galaxy to first transparently index it using `bwa index` command, and then run\n+     mapping with `bwa aln`.\n+\n+\n If your genome of interest is not listed here you have two choices:\n \n-  1. Contact galaxy team using **Help->Support** link at the top of the interface and let us know that an index needs to be added\n-  2. Upload your genome of interest as a FASTA file to Galaxy history and selected **Use a genome from the history and build index** option.\n-\n------\n-\n-**Galaxy-specific option**\n-\n-Galaxy allows three levels of control over bwa-mem options provided by **Select analysis mode** menu option. These are:\n-\n-  1. *Simple Illumina mode*: The simplest possible bwa mem application in which it alignes single or paired-end data to reference using default parameters. It is equivalent to the following command: bwa mem &lt;reference index&gt; &lt;fastq dataset1&gt; [fastq dataset2]\n-  2. *Full list of options*: Allows access to all options through Galaxy interface.\n-\n-------\n-\n-**bwa-aln options**\n-\n-Each Galaxy parameter widget corresponds to command line flags listed below::\n+  1. Contact galaxy team using **Help->Support** link at the top of the interface and let us know that an index\n+     needs to be added\n+  2. Upload your genome of interest as a FASTA file to Galaxy history and selected **Use a genome from the history\n+     and build index** option.\n \n-    -n NUM    max #diff (int) or missing prob under 0.02 err rate (float) [0.04]\n-    -o INT    maximum number or fraction of gap opens [1]\n-    -e INT    maximum number of gap extensions, -1 for disabling long gaps [-1]\n-    -i INT    do not put an indel within INT bp towards the ends [5]\n-    -d INT    maximum occurrences for extending a long deletion [10]\n-    -l INT    seed length [32]\n-    -k INT    maximum differences in the seed [2]\n-    -m INT    maximum entries in the queue [2000000]\n-    -M INT    mismatch penalty [3]\n-    -O INT    gap open penalty [11]\n-    -E INT    gap extension penalty [4]\n-    -R INT    stop searching when there are >INT equally best hits [30]\n-    -q INT    quality threshold for read trimming down to 35bp [0]\n-    -B INT    length of barcode\n-    -L        log-scaled gap penalty for long deletions\n-    -N        non-iterative mode: search for all n-difference hits (slooow)\n-    -I        the input is in the Illumina 1.3+ FASTQ-like format\n-    -b        the input read file is in the BAM format\n-    -0        use single-end reads only (effective with -b)\n-    -1        use the 1st read in a pair (effective with -b)\n-    -2        use the 2nd read in a pair (effective with -b)\n-\n-**bwa-samse options**::\n-\n-    -a INT    maximum insert size [500]\n-    -o INT    maximum occurrences for one end [100000]\n-    -n INT    maximum hits to output for paired reads [3]\n-    -N INT    maximum hits to output for discordant pairs [10]\n-    -c FLOAT  prior of chimeric rate (lower bound) [1.0e-05]\n-    -r STR    read group header line [null]\n-\n-**bwa-sampe options**::\n-\n-    -n INT    maximum hits to output for paired reads [3]\n-    -r STR    read group header line [null]\n-\n-@dataset_collections@\n \n @RG@\n \n @info@\n-  </help>\n-  <citations>\n-    <citation type="doi">10.1093/bioinformatics/btp324</citation>\n-    <citation type="doi">10.1093/bioinformatics/btp698</citation>\n-  </citations>\n+    ]]></help>\n+    <citations>\n+        <citation type="doi">10.1093/bioinformatics/btp324</citation>\n+        <citation type="doi">10.1093/bioinformatics/btp698</citation>\n+    </citations>\n </tool>\n'
b
diff -r d1228ec6233f -r 48f306c57611 bwa_macros.xml
--- a/bwa_macros.xml Tue Nov 21 11:24:01 2017 -0500
+++ b/bwa_macros.xml Fri Nov 24 09:55:45 2017 -0500
[
b'@@ -1,115 +1,115 @@\n <macros>\n-  <import>read_group_macros.xml</import>\n+    <import>read_group_macros.xml</import>\n \n-  <token name="@VERSION@">0.7.17</token>\n+    <token name="@VERSION@">0.7.17</token>\n \n-  <token name="@set_rg_string@">\n-      #set $rg_string = "@RG\\\\tID:" + str($rg_id)\n-      #set $rg_string += $format_read_group("\\\\tSM:", $rg_sm)\n-      #set $rg_string += $format_read_group("\\\\tPL:", $rg_pl)\n-      #set $rg_string += $format_read_group("\\\\tLB:", $rg_lb)\n-      #set $rg_string += $format_read_group("\\\\tCN:", $rg_cn)\n-      #set $rg_string += $format_read_group("\\\\tDS:", $rg_ds)\n-      #set $rg_string += $format_read_group("\\\\tDT:", $rg_dt)\n-      #set $rg_string += $format_read_group("\\\\tFO:", $rg_fo)\n-      #set $rg_string += $format_read_group("\\\\tKS:", $rg_ks)\n-      #set $rg_string += $format_read_group("\\\\tPG:", $rg_pg)\n-      #set $rg_string += $format_read_group("\\\\tPI:", $rg_pi)\n-      #set $rg_string += $format_read_group("\\\\tPU:", $rg_pu)\n-  </token>\n+    <token name="@set_rg_string@">\n+        #set $rg_string = "@RG\\\\tID:" + str($rg_id)\n+        #set $rg_string += $format_read_group("\\\\tSM:", $rg_sm)\n+        #set $rg_string += $format_read_group("\\\\tPL:", $rg_pl)\n+        #set $rg_string += $format_read_group("\\\\tLB:", $rg_lb)\n+        #set $rg_string += $format_read_group("\\\\tCN:", $rg_cn)\n+        #set $rg_string += $format_read_group("\\\\tDS:", $rg_ds)\n+        #set $rg_string += $format_read_group("\\\\tDT:", $rg_dt)\n+        #set $rg_string += $format_read_group("\\\\tFO:", $rg_fo)\n+        #set $rg_string += $format_read_group("\\\\tKS:", $rg_ks)\n+        #set $rg_string += $format_read_group("\\\\tPG:", $rg_pg)\n+        #set $rg_string += $format_read_group("\\\\tPI:", $rg_pi)\n+        #set $rg_string += $format_read_group("\\\\tPU:", $rg_pu)\n+    </token>\n \n-  <token name="@set_reference_fasta_filename@"><![CDATA[\n+    <token name="@set_reference_fasta_filename@"><![CDATA[\n     #if str( $reference_source.reference_source_selector ) == "history":\n         #set $reference_fasta_filename = "localref.fa"\n-        ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &&\n+        ln -s \'${reference_source.ref_file}\' \'${reference_fasta_filename}\' &&\n         bwa index\n         #if str($reference_source.index_a) != \'auto\'\n             -a ${reference_source.index_a}\n         #end if\n-        "${reference_fasta_filename}" &&\n+        \'${reference_fasta_filename}\' &&\n     #else:\n         #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )\n     #end if\n   ]]></token>\n \n-  <xml name="requirements">\n-    <requirements>\n-      <requirement type="package" version="@VERSION@">bwa</requirement>\n-      <requirement type="package" version="1.5">samtools</requirement>\n-    </requirements>\n-  </xml>\n+    <xml name="requirements">\n+        <requirements>\n+            <requirement type="package" version="@VERSION@">bwa</requirement>\n+            <requirement type="package" version="1.6">samtools</requirement>\n+        </requirements>\n+    </xml>\n \n-  <xml name="stdio">\n-      <stdio>\n-          <exit_code range="1:" />\n-          <exit_code range=":-1" />\n-          <regex match="Error:" />\n-          <regex match="Exception:" />\n-      </stdio>\n-  </xml>\n+    <xml name="stdio">\n+        <stdio>\n+            <exit_code range="1:" />\n+            <exit_code range=":-1" />\n+            <regex match="Error:" />\n+            <regex match="Exception:" />\n+        </stdio>\n+    </xml>\n \n-  <macro name="reference_source_conditional">\n-    <conditional name="reference_source">\n-      <param name="reference_source_selector" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options. See `Indexes` section of help below">\n-        <option value="cached">Use a built-in genome index</option>\n-        <option value="history">Use a genome from history and build index</option>\n-      </param>\n-      <when va'..b'7N memory where N is the size of the database. IS is moderately fast, but does not work with database larger than 2GB</option>\n+                    <option value="bwtsw">BWT-SW algorithm. This method works also with big genomes</option>\n+                </param>\n+            </when>\n+        </conditional>\n+    </macro>\n \n-  <macro name="dbKeyActionsBwa">\n-    <expand macro="dbKeyActions">\n-      <option type="from_data_table" name="bwa_indexes" column="1" offset="0">\n-        <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>\n-        <filter type="param_value" ref="reference_source.ref_file" column="0"/>\n-      </option>\n-    </expand>\n-  </macro>\n+    <macro name="dbKeyActionsBwa">\n+        <expand macro="dbKeyActions">\n+            <option type="from_data_table" name="bwa_indexes" column="1" offset="0">\n+                <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>\n+                <filter type="param_value" ref="reference_source.ref_file" column="0"/>\n+            </option>\n+        </expand>\n+    </macro>\n \n-  <macro name="dbKeyActionsBwaMem">\n-    <expand macro="dbKeyActions">\n-      <option type="from_data_table" name="bwa_mem_indexes" column="1" offset="0">\n-        <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>\n-        <filter type="param_value" ref="reference_source.ref_file" column="0"/>\n-      </option>\n-    </expand>\n-  </macro>\n+    <macro name="dbKeyActionsBwaMem">\n+        <expand macro="dbKeyActions">\n+            <option type="from_data_table" name="bwa_mem_indexes" column="1" offset="0">\n+                <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>\n+                <filter type="param_value" ref="reference_source.ref_file" column="0"/>\n+            </option>\n+        </expand>\n+    </macro>\n \n-  <macro name="dbKeyActions">\n-      <actions>\n-          <conditional name="reference_source.reference_source_selector">\n-              <when value="cached">\n-                  <action type="metadata" name="dbkey">\n-                      <yield />\n-                  </action>\n-              </when>\n-              <when value="history">\n-                  <action type="metadata" name="dbkey">\n-                    <option type="from_param" name="reference_source.ref_file" param_attribute="dbkey" />\n-                  </action>\n-              </when>\n-          </conditional>\n-      </actions>\n-  </macro>\n+    <macro name="dbKeyActions">\n+        <actions>\n+            <conditional name="reference_source.reference_source_selector">\n+                <when value="cached">\n+                    <action type="metadata" name="dbkey">\n+                        <yield />\n+                    </action>\n+                </when>\n+                <when value="history">\n+                    <action type="metadata" name="dbkey">\n+                        <option type="from_param" name="reference_source.ref_file" param_attribute="dbkey" />\n+                    </action>\n+                </when>\n+            </conditional>\n+        </actions>\n+    </macro>\n \n-  <token name="@RG@">\n+    <token name="@RG@">\n -----\n \n .. class:: warningmark\n@@ -160,8 +160,8 @@\n  @RG     ID:FLOWCELL2.LANE4      PL:illumina     LB:LIB-KID-2 SM:KID      PI:400\n \n Note the hierarchical relationship between read groups (unique for each lane) to libraries (sequenced on two lanes) and samples (across four lanes, two lanes for each library).\n-  </token>\n-  <token name="@info@">    \n+    </token>\n+    <token name="@info@">\n -----\n \n .. class:: infomark\n@@ -175,16 +175,5 @@\n   3. https://github.com/lh3/bwa\n   4. http://bio-bwa.sourceforge.net/\n \n-  </token>\n-\n-  <token name="@dataset_collections@">\n-------\n-\n-**Dataset collections - processing large numbers of datasets at once**\n-\n-Dataset collections are in beta-testing. Extensive documentation will be added later this Spring.\n-\n-\n-  </token>\n-\n+    </token>\n </macros>\n'