Mercurial > repos > iuc > tetyper
changeset 1:36093854bfc7 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
| author | iuc |
|---|---|
| date | Sat, 18 Jan 2020 15:04:39 -0500 |
| parents | 8bc80c2a15b3 |
| children | edcf603bedfd |
| files | test-data/tetyper_snp_profiles.loc test-data/tetyper_struct_profiles.loc tetyper.xml tool-data/tetyper_snp_profiles.loc.sample tool-data/tetyper_struct_profiles.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
| diffstat | 7 files changed, 124 insertions(+), 9 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tetyper_snp_profiles.loc Sat Jan 18 15:04:39 2020 -0500 @@ -0,0 +1,6 @@ +# Tab separated with three columns: +# - value (Galaxy records this in the Galaxy DB) +# - name (Galaxy shows this in the UI) +# - path (path to the snp_profiles.txt file) +# +Tn4401b_snp_profiles "Tn4401b SNP Profiles" ${__HERE__}/Tn4401b_snp_profiles.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tetyper_struct_profiles.loc Sat Jan 18 15:04:39 2020 -0500 @@ -0,0 +1,6 @@ +# Tab separated with three columns: +# - value (Galaxy records this in the Galaxy DB) +# - name (Galaxy shows this in the UI) +# - path (path to the struct_profiles.txt file) +# +Tn4401b_struct_profiles "Tn4401b Structural Variant Profiles" ${__HERE__}/Tn4401b_struct_profiles.txt
--- a/tetyper.xml Thu Nov 28 14:41:08 2019 -0500 +++ b/tetyper.xml Sat Jan 18 15:04:39 2020 -0500 @@ -1,4 +1,4 @@ -<tool id="tetyper" name="TETyper" version="@TOOL_VERSION@+galaxy0"> +<tool id="tetyper" name="TETyper" version="@TOOL_VERSION@+galaxy1"> <description>Transposable Element Typer</description> <macros> <token name="@TOOL_VERSION@">1.1</token> @@ -21,11 +21,15 @@ --min_each_strand '${min_each_strand}' --min_mapped_len '${min_mapped_len}' --min_qual '${min_qual}' - #if $snp_profiles - --snp_profiles '${snp_profiles}' + #if str( $snp_profiles_source.snp_profiles_source_selector ) == "tool_data_table": + --snp_profiles '$snp_profiles_source.snp_profiles.fields.path' + #elif str( $snp_profiles_source.snp_profiles_source_selector ) == 'history': + --snp_profiles '$snp_profiles_source.snp_profiles' #end if - #if $struct_profiles - --struct_profiles '${struct_profiles}' + #if str( $struct_profiles_source.struct_profiles_source_selector ) == "tool_data_table": + --struct_profiles '$struct_profiles_source.struct_profiles.fields.path' + #elif str( $struct_profiles_source.struct_profiles_source_selector ) == 'history': + --struct_profiles '$struct_profiles_source.struct_profiles' #end if --outprefix output ]]> @@ -44,14 +48,54 @@ <param format="fastq,fastq.gz" name="reverse_input" type="data" label="Reverse strand" help="FASTQ dataset"/> </when> </conditional> + <conditional name="snp_profiles_source"> + <param name="snp_profiles_source_selector" type="select" + label="Select a SNP profile from your history or use one from a tool data table?"> + <option value="No" selected="true">No SNP profile</option> + <option value="tool_data_table">SNP profile from tool data table</option> + <option value="history">SNP profile from history</option> + </param> + <when value="No"/> + <when value="tool_data_table"> + <param name="snp_profiles" type="select" format="tabular" label="SNP Profile"> + <options from_data_table="tetyper_snp_profiles"> + <validator type="no_options" message="No TETyper SNP profiles are available" /> + </options> + </param> + </when> + <when value="history"> + <param name="snp_profiles" type="data" format="tabular" label="SNP Profile" + help="A three-column tabular file with SNP profile definitions"/> + </when> + </conditional> + <conditional name="struct_profiles_source"> + <param name="struct_profiles_source_selector" type="select" + label="Select a structural variant profile from your history or use one from a tool data table?"> + <option value="No" selected="true">No structural variant profile</option> + <option value="tool_data_table">Structural variant profile from tool data table</option> + <option value="history" selected="true">Structural variant profile from history</option> + </param> + <when value="No"/> + <when value="tool_data_table"> + <param name="struct_profiles" type="select" format="tabular" + label="Structural Variant Profile"> + <options from_data_table="tetyper_struct_profiles"> + <validator type="no_options" message="No TETyper structural variant profiles are available" /> + </options> + </param> + </when> + <when value="history"> + <param name="struct_profiles" type="data" format="tabular" + label="Structural Variant Profile" + help="A two-column tabular file with structural variant profile definitions"/> + </when> + </conditional> <param name="reference" type="data" format="fasta" label="Transposable Element Reference"/> <param name="flank_length" type="integer" min="4" value="5" max="16" label="Flank Length" help="Length of flanking region to extract."/> <param name="min_reads" type="integer" min="1" value="10" max="100" label="Minimum Reads" help="Minimum read number for including a specific flanking sequence."/> <param name="min_each_strand" type="integer" min="1" value="1" max="100" label="Minimum Reads (each strand)" help="Minimum read number for each strand for including a specific flanking sequence."/> <param name="min_mapped_len" type="integer" min="8" value="30" max="100" label="Minimum Mapped Length" help="Minimum length of mapping for a read to be used in determining flanking sequences. Higher values are more robust to spurious mapping. Lower values will recover more reads."/> <param name="min_qual" type="integer" min="0" value="10" max="100" label="Minimum quality" help="Minimum quality value across extracted flanking sequence." /> - <param name="snp_profiles" type="data" format="text" label="SNP Profiles" optional="true" /> - <param name="struct_profiles" type="data" format="text" label="Structural Variant Profiles" optional="true" /> <param name="include_log" type="boolean" label="Include log in output"/> </inputs> <outputs> @@ -80,8 +124,31 @@ <param name="forward_input" value="ERR1911133_Tn4401b-1_mapped_subsampled_1.fastq" /> <param name="reverse_input" value="ERR1911133_Tn4401b-1_mapped_subsampled_2.fastq" /> </conditional> - <param name="snp_profiles" value="Tn4401b_snp_profiles.txt" /> - <param name="struct_profiles" value="Tn4401b_struct_profiles.txt" /> + <conditional name="snp_profiles_source"> + <param name="snp_profiles_source_selector" value="history" /> + <param name="snp_profiles" value="Tn4401b_snp_profiles.txt" /> + </conditional> + <conditional name="struct_profiles_source"> + <param name="struct_profiles_source_selector" value="history" /> + <param name="struct_profiles" value="Tn4401b_struct_profiles.txt" /> + </conditional> + <output name="summary" file="output_summary_2.txt" /> + </test> + <test> + <param name="reference" value="Tn4401b-1.fasta" /> + <conditional name="collection_paired"> + <param name="selector" value="paired" /> + <param name="forward_input" value="ERR1911133_Tn4401b-1_mapped_subsampled_1.fastq" /> + <param name="reverse_input" value="ERR1911133_Tn4401b-1_mapped_subsampled_2.fastq" /> + </conditional> + <conditional name="snp_profiles_source"> + <param name="snp_profiles_source_selector" value="tool_data_table" /> + <param name="snp_profiles" value="Tn4401b_snp_profiles" /> + </conditional> + <conditional name="struct_profiles_source"> + <param name="struct_profiles_source_selector" value="tool_data_table" /> + <param name="struct_profiles" value="Tn4401b_struct_profiles" /> + </conditional> <output name="summary" file="output_summary_2.txt" /> </test> </tests>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/tetyper_snp_profiles.loc.sample Sat Jan 18 15:04:39 2020 -0500 @@ -0,0 +1,7 @@ +# Expect three columns, tab separated, as follows: +# - value (Galaxy records this in the Galaxy DB, must be unique, suggest using a UUID) +# - name (Galaxy shows this in the UI) +# - path to snp_profiles.txt file +# +# e.g. +# c4269788-80f0-4ed5-9ff4-5fe30484678d<tab>SNP Profiles<tab>/path/to/tetyper/snp_profiles.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/tetyper_struct_profiles.loc.sample Sat Jan 18 15:04:39 2020 -0500 @@ -0,0 +1,7 @@ +# Expect three columns, tab separated, as follows: +# - value (Galaxy records this in the Galaxy DB, must be unique, suggest using a UUID) +# - name (Galaxy shows this in the UI) +# - path to struct_profiles.txt file +# +# e.g. +# e6987a4f-c54b-490e-a32d-67e91e0c2328<tab>Structural Variant Profiles<tab>/path/to/tetyper/struct_profiles.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Sat Jan 18 15:04:39 2020 -0500 @@ -0,0 +1,11 @@ +<?xml version="1.0"?> +<tables> + <table name="tetyper_snp_profiles" comment_char="#"> + <columns>value, name, path</columns> + <file path="tool-data/tetyper_snp_profiles.loc" /> + </table> + <table name="tetyper_struct_profiles" comment_char="#"> + <columns>value, name, path</columns> + <file path="tool-data/tetyper_struct_profiles.loc" /> + </table> +</tables>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Sat Jan 18 15:04:39 2020 -0500 @@ -0,0 +1,11 @@ +<?xml version="1.0"?> +<tables> + <table name="tetyper_snp_profiles" comment_char="#"> + <columns>value, name, path</columns> + <file path="${__HERE__}/test-data/tetyper_snp_profiles.loc" /> + </table> + <table name="tetyper_struct_profiles" comment_char="#"> + <columns>value, name, path</columns> + <file path="${__HERE__}/test-data/tetyper_struct_profiles.loc" /> + </table> +</tables>