| Previous changeset 5:fbf460831036 (2015-07-21) Next changeset 7:d8c9597bfb09 (2015-11-03) |
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Commit message:
planemo upload commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty |
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modified:
bwa-mem.xml bwa.xml bwa_macros.xml read_group_macros.xml |
| b |
| diff -r fbf460831036 -r 09a7281d24c5 bwa-mem.xml --- a/bwa-mem.xml Tue Jul 21 13:51:02 2015 -0400 +++ b/bwa-mem.xml Tue Jul 21 14:12:49 2015 -0400 |
| b |
| @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="bwa_mem" name="Map with BWA-MEM" version="0.3"> +<tool id="bwa_mem" name="Map with BWA-MEM" version="0.3.1"> <description>- map medium and long reads (> 100 bp) against reference genome</description> <macros> <import>read_group_macros.xml</import> @@ -9,9 +9,7 @@ <requirement type="package" version="0.7.10.039ea20639">bwa</requirement> <requirement type="package" version="1.1">samtools</requirement> </requirements> - <stdio> - <exit_code range="1:" /> - </stdio> + <expand macro="stdio" /> <command> #set $reference_fasta_filename = "localref.fa" @@ -291,7 +289,9 @@ </inputs> <outputs> - <data format="bam" name="bam_output" label="${tool.name} on ${on_string} (mapped reads in BAM format)"/> + <data format="bam" name="bam_output" label="${tool.name} on ${on_string} (mapped reads in BAM format)"> + <expand macro="dbKeyActionsBwaMem" /> + </data> </outputs> <tests> |
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| diff -r fbf460831036 -r 09a7281d24c5 bwa.xml --- a/bwa.xml Tue Jul 21 13:51:02 2015 -0400 +++ b/bwa.xml Tue Jul 21 14:12:49 2015 -0400 |
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| @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="bwa" name="Map with BWA" version="0.3.0"> +<tool id="bwa" name="Map with BWA" version="0.3.1"> <description>- map short reads (< 100 bp) against reference genome</description> <macros> <import>read_group_macros.xml</import> @@ -70,9 +70,7 @@ <requirement type="package" version="0.7.10.039ea20639">bwa</requirement> <requirement type="package" version="1.1">samtools</requirement> </requirements> - <stdio> - <exit_code range="1:" /> - </stdio> + <expand macro="stdio" /> <command> #set $reference_fasta_filename = "localref.fa" @@ -371,7 +369,9 @@ </inputs> <outputs> - <data format="bam" name="bam_output" label="${tool.name} on ${on_string} (mapped reads in BAM format)"/> + <data format="bam" name="bam_output" label="${tool.name} on ${on_string} (mapped reads in BAM format)"> + <expand macro="dbKeyActionsBwa" /> + </data> </outputs> <tests> |
| b |
| diff -r fbf460831036 -r 09a7281d24c5 bwa_macros.xml --- a/bwa_macros.xml Tue Jul 21 13:51:02 2015 -0400 +++ b/bwa_macros.xml Tue Jul 21 14:12:49 2015 -0400 |
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| @@ -14,7 +14,51 @@ #set $rg_string += $format_read_group("\tPI:", $rg_pi) #set $rg_string += $format_read_group("\tPU:", $rg_pu) </token> - + + <xml name="stdio"> + <stdio> + <exit_code range="1:" /> + <exit_code range=":-1" /> + <regex match="Error:" /> + <regex match="Exception:" /> + </stdio> + </xml> + + <macro name="dbKeyActionsBwa"> + <expand macro="dbKeyActions"> + <option type="from_data_table" name="bwa_indexes" column="1" offset="0"> + <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> + <filter type="param_value" ref="reference_source.ref_file" column="0"/> + </option> + </expand> + </macro> + + <macro name="dbKeyActionsBwaMem"> + <expand macro="dbKeyActions"> + <option type="from_data_table" name="bwa_mem_indexes" column="1" offset="0"> + <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> + <filter type="param_value" ref="reference_source.ref_file" column="0"/> + </option> + </expand> + </macro> + + <macro name="dbKeyActions"> + <actions> + <conditional name="reference_source.reference_source_selector"> + <when value="cached"> + <action type="metadata" name="dbkey"> + <yield /> + </action> + </when> + <when value="history"> + <action type="metadata" name="dbkey"> + <option type="from_param" name="reference_source.ref_file" param_attribute="dbkey" /> + </action> + </when> + </conditional> + </actions> + </macro> + <token name="@RG@"> ----- |
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| diff -r fbf460831036 -r 09a7281d24c5 read_group_macros.xml --- a/read_group_macros.xml Tue Jul 21 13:51:02 2015 -0400 +++ b/read_group_macros.xml Tue Jul 21 14:12:49 2015 -0400 |
| [ |
| @@ -2,7 +2,6 @@ <!-- Import this at the top of your command block and then define rg_auto_name. --> <token name="@define_read_group_helpers@"> -#import re #def identifier_or_name($input1) #if hasattr($input1, 'element_identifier') #return $input1.element_identifier @@ -12,6 +11,7 @@ #end def #def clean(name) + #import re #set $name_clean = re.sub('[^\w\-_\.]', '_', $name) #return $name_clean #end def @@ -79,7 +79,7 @@ #if $rg_param('read_group_lb_conditional') is None #set $rg_lb = '' - #elif $rg_param('read_group_lb_conditional')do_auto_name + #elif $rg_param('read_group_lb_conditional').do_auto_name #set $rg_lb = $rg_auto_name #else #set $rg_lb = str($rg_param('read_group_lb_conditional').LB) @@ -147,7 +147,7 @@ </xml> <xml name="read_group_id_param"> <param name="ID" type="text" value="" size="20" label="Read group identifier (ID)" help="This value must be unique among multiple samples in your experiment" optional="false"> - <validator type="empty_field" /> + <validator type="empty_field" /> </param> </xml> <xml name="read_group_id_conditional"> |