From f865e8359fa6c8d599011edcea61a2a728afb9ea Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Mon, 10 Sep 2018 11:09:57 +0100 Subject: [PATCH] Deprecate `size` attribute of `` and remove it from tools Also: - dos2unix test/functional/tools/for_workflows/head.xml - Single-quote text and data params in `` - Remove deprecated `interpreter` attribute of `` --- config/job_resource_params_conf.xml.sample | 6 +- .../workflow_resource_params_conf.xml.sample | 6 +- lib/galaxy/tools/parameters/validation.py | 8 +- lib/galaxy/tools/xsd/galaxy.xsd | 34 ++++---- test/functional/tools/for_workflows/head.xml | 26 +++---- test/unit/tools/test_wrappers.py | 2 +- tools/data_source/genbank.xml | 4 +- tools/data_source/upload.xml | 37 ++++----- tools/extract/liftOver_wrapper.xml | 8 +- tools/filters/CreateInterval.xml | 18 ++--- tools/filters/bed_to_bigbed.xml | 4 +- tools/filters/changeCase.xml | 12 +-- tools/filters/fileGrep.xml | 17 ++-- tools/filters/fixedValueColumn.xml | 16 ++-- tools/filters/gff/gff_filter_by_attribute.xml | 14 ++-- .../gff/gff_filter_by_feature_count.xml | 15 ++-- tools/filters/grep.xml | 2 +- tools/filters/headWrapper.xml | 12 +-- tools/filters/randomlines.xml | 10 +-- tools/filters/remove_beginning.xml | 14 ++-- tools/filters/tailWrapper.xml | 8 +- tools/filters/wig_to_bigwig.xml | 4 +- tools/maf/vcf_to_maf_customtrack.xml | 2 +- tools/metag_tools/blat_wrapper.xml | 6 +- tools/metag_tools/shrimp_color_wrapper.xml | 34 ++++---- tools/metag_tools/shrimp_wrapper.xml | 32 ++++---- tools/plotting/bar_chart.xml | 26 ++++--- tools/plotting/boxplot.xml | 6 +- tools/solid_tools/maq_cs_wrapper.xml | 77 +++++++++---------- tools/sr_mapping/PerM.xml | 12 +-- tools/sr_mapping/bfast_wrapper.xml | 2 +- tools/stats/filtering.xml | 2 +- tools/stats/gsummary.xml | 16 ++-- tools/stats/gsummary.xml.groups | 20 +++-- 34 files changed, 244 insertions(+), 268 deletions(-) diff --git a/config/job_resource_params_conf.xml.sample b/config/job_resource_params_conf.xml.sample index 9a201c8f4bb..c9adce5cb97 100644 --- a/config/job_resource_params_conf.xml.sample +++ b/config/job_resource_params_conf.xml.sample @@ -1,6 +1,6 @@ - - - + + + diff --git a/config/workflow_resource_params_conf.xml.sample b/config/workflow_resource_params_conf.xml.sample index c04d2909aa5..0495c2443ed 100644 --- a/config/workflow_resource_params_conf.xml.sample +++ b/config/workflow_resource_params_conf.xml.sample @@ -1,7 +1,7 @@ - - - + + + - - + + @@ -17,13 +17,13 @@ python '$__tool_directory__/random_lines_two_pass.py' '${input}' '${out_file1}' - + - + @@ -41,7 +41,6 @@ python '$__tool_directory__/random_lines_two_pass.py' '${input}' '${out_file1}' - **What it does** This tool selects N random lines from a file, with no repeats, and preserving ordering. @@ -62,6 +61,5 @@ Selecting 2 random lines might return this:: chr7 56736 56756 D17003_CTCF_R7 354 + chr7 56775 56795 D17003_CTCF_R4 207 + - diff --git a/tools/filters/remove_beginning.xml b/tools/filters/remove_beginning.xml index a929e483d83..2a1023f710b 100644 --- a/tools/filters/remove_beginning.xml +++ b/tools/filters/remove_beginning.xml @@ -1,12 +1,14 @@ of a file - remove_beginning.pl $input $num_lines $out_file1 + +perl '$__tool_directory__/remove_beginning.pl' '$input' $num_lines '$out_file1' + - - + + - + @@ -16,7 +18,6 @@ - **What it does** This tool removes a specified number of lines from the beginning of a dataset. @@ -37,6 +38,5 @@ After removing the first 3 lines the dataset will look like this:: chr7 56772 56792 D17003_CTCF_R7 372 + chr7 56775 56795 D17003_CTCF_R4 207 + - - + diff --git a/tools/filters/tailWrapper.xml b/tools/filters/tailWrapper.xml index 0865145dc88..166018ec1d2 100644 --- a/tools/filters/tailWrapper.xml +++ b/tools/filters/tailWrapper.xml @@ -3,11 +3,11 @@ perl '$__tool_directory__/tailWrapper.pl' '$input' $lineNum '$out_file1' - - + + - + @@ -17,7 +17,6 @@ perl '$__tool_directory__/tailWrapper.pl' '$input' $lineNum '$out_file1' - **What it does** This tool outputs specified number of lines from the **end** of a dataset @@ -38,6 +37,5 @@ This tool outputs specified number of lines from the **end** of a dataset chr7 57341 57361 D17003_CTCF_R7 375 + chr7 57457 57477 D17003_CTCF_R3 188 + - diff --git a/tools/filters/wig_to_bigwig.xml b/tools/filters/wig_to_bigwig.xml index 7db6785af6a..5e99e922722 100644 --- a/tools/filters/wig_to_bigwig.xml +++ b/tools/filters/wig_to_bigwig.xml @@ -31,8 +31,8 @@ - - + + diff --git a/tools/maf/vcf_to_maf_customtrack.xml b/tools/maf/vcf_to_maf_customtrack.xml index 3fbe06513cf..c10618ac41e 100644 --- a/tools/maf/vcf_to_maf_customtrack.xml +++ b/tools/maf/vcf_to_maf_customtrack.xml @@ -20,7 +20,7 @@ ${vcf_source_type.vcf_source} -n '$track_name' -g - + diff --git a/tools/metag_tools/blat_wrapper.xml b/tools/metag_tools/blat_wrapper.xml index f018f1a7b39..1171c524a61 100644 --- a/tools/metag_tools/blat_wrapper.xml +++ b/tools/metag_tools/blat_wrapper.xml @@ -19,9 +19,9 @@ - - - + + + diff --git a/tools/metag_tools/shrimp_color_wrapper.xml b/tools/metag_tools/shrimp_color_wrapper.xml index 55e72415659..c2b4379bf9d 100644 --- a/tools/metag_tools/shrimp_color_wrapper.xml +++ b/tools/metag_tools/shrimp_color_wrapper.xml @@ -19,23 +19,23 @@ python '$__tool_directory__/shrimp_color_wrapper.py' '$input_target' '$input_que - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + diff --git a/tools/metag_tools/shrimp_wrapper.xml b/tools/metag_tools/shrimp_wrapper.xml index f88180c5dc7..d4c974cf41a 100644 --- a/tools/metag_tools/shrimp_wrapper.xml +++ b/tools/metag_tools/shrimp_wrapper.xml @@ -25,7 +25,7 @@ python '$__tool_directory__/shrimp_wrapper.py' '$input_target' '$output1' '$outp - + @@ -38,21 +38,21 @@ python '$__tool_directory__/shrimp_wrapper.py' '$input_target' '$output1' '$outp - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + diff --git a/tools/plotting/bar_chart.xml b/tools/plotting/bar_chart.xml index 7d2855d0445..b9447a49a35 100644 --- a/tools/plotting/bar_chart.xml +++ b/tools/plotting/bar_chart.xml @@ -1,9 +1,13 @@ for multiple columns - - #if $xtic.userSpecified == "Yes" #bar_chart.py $input $xtic.xticColumn $colList "$title" "$ylabel" $ymin $ymax $out_file1 "$pdf_size" - #else #bar_chart.py $input 0 $colList "$title" "$ylabel" $ymin $ymax $out_file1 "$pdf_size" - #end if + +python '$__tool_directory__/bar_chart.py' '$input' +#if $xtic.userSpecified == "Yes" + $xtic.xticColumn +#else + 0 +#end if +$colList '$title' '$ylabel' $ymin $ymax '$out_file1' '$pdf_size' @@ -18,11 +22,11 @@ - - - - - + + + + + @@ -33,7 +37,7 @@ - + gnuplot-py @@ -53,5 +57,5 @@ Graphing columns 2 and 3 while using column 1 for X Tick Labels will produce the .. image:: ${static_path}/images/bar_chart.png :height: 324 :width: 540 - + diff --git a/tools/plotting/boxplot.xml b/tools/plotting/boxplot.xml index 415e02e2f8c..9c59980ec23 100644 --- a/tools/plotting/boxplot.xml +++ b/tools/plotting/boxplot.xml @@ -6,10 +6,10 @@ - + - - + + diff --git a/tools/solid_tools/maq_cs_wrapper.xml b/tools/solid_tools/maq_cs_wrapper.xml index 8fe3fb7e68e..a3d3ec04cbf 100644 --- a/tools/solid_tools/maq_cs_wrapper.xml +++ b/tools/solid_tools/maq_cs_wrapper.xml @@ -1,56 +1,53 @@ - - maq_cs_wrapper.py - $output1 - $output2 - $ref - $library_type.f3_reads - $library_type.f3_qual - $library_type.is_paired - #if $library_type.is_paired == "yes": - $library_type.r3_reads - $library_type.r3_qual - #else: - "None" - "None" - #end if - $min_mapqual - $max_mismatch - $output3 - + +python '$__tool_directory__/maq_cs_wrapper.py' +'$output1' +'$output2' +'$ref' +'$library_type.f3_reads' +'$library_type.f3_qual' +$library_type.is_paired +#if $library_type.is_paired == "yes": + '$library_type.r3_reads' + '$library_type.r3_qual' +#else: + "None" + "None" +#end if +$min_mapqual +$max_mismatch +'$output3' - + - - + + - - - - + + + + - - + + - - - + + + - - .. class:: infomark **What it does** -This tool maps SOLiD color-space reads against the target genome using MAQ. It produces three output datasets: +This tool maps SOLiD color-space reads against the target genome using MAQ. It produces three output datasets: -**ALIGNMENT INFO** : contains the read alignment information, +**ALIGNMENT INFO** : contains the read alignment information, **PILEUP** : contains the coverage and SNP statistics for every nucleotide of the target genome, -**CUSTOM TRACK** : contains the coverage and SNP statistics as custom tracks displayable in the UCSC browser. +**CUSTOM TRACK** : contains the coverage and SNP statistics as custom tracks displayable in the UCSC browser. ----- @@ -113,8 +108,6 @@ This tool maps SOLiD color-space reads against the target genome using MAQ. It p * column 7 = number of Ts * column 8 = number of Gs * column 9 = number of Cs - - - - + + diff --git a/tools/sr_mapping/PerM.xml b/tools/sr_mapping/PerM.xml index d0b84ea11fe..1df2dcd570d 100644 --- a/tools/sr_mapping/PerM.xml +++ b/tools/sr_mapping/PerM.xml @@ -84,8 +84,8 @@ - - + + @@ -116,14 +116,14 @@ - - + + - + @@ -147,7 +147,7 @@ - + diff --git a/tools/sr_mapping/bfast_wrapper.xml b/tools/sr_mapping/bfast_wrapper.xml index 4c28721990d..c901969d7e8 100644 --- a/tools/sr_mapping/bfast_wrapper.xml +++ b/tools/sr_mapping/bfast_wrapper.xml @@ -72,7 +72,7 @@ - + diff --git a/tools/stats/filtering.xml b/tools/stats/filtering.xml index 460479e664f..1a20cf40c94 100644 --- a/tools/stats/filtering.xml +++ b/tools/stats/filtering.xml @@ -11,7 +11,7 @@ - + diff --git a/tools/stats/gsummary.xml b/tools/stats/gsummary.xml index f7168d2400b..b314c8671e2 100644 --- a/tools/stats/gsummary.xml +++ b/tools/stats/gsummary.xml @@ -9,25 +9,26 @@ - python $__tool_directory__/gsummary.py "$input" "$out_file1" "$cond" + +python '$__tool_directory__/gsummary.py' '$input' '$out_file1' '$cond' + - - + + - + - + - .. class:: warningmark This tool expects input datasets consisting of tab-delimited columns (blank or comment lines beginning with a # character are automatically skipped). @@ -77,6 +78,5 @@ This tool computes basic summary statistics on a given column, or on a valid exp #sum mean stdev 0% 25% 50% 75% 100% 29250.000 7312.500 7198.636 1700.000 1895.000 5280.000 10697.500 16990.000 - - + diff --git a/tools/stats/gsummary.xml.groups b/tools/stats/gsummary.xml.groups index 218ab31aa38..b043ed5682e 100644 --- a/tools/stats/gsummary.xml.groups +++ b/tools/stats/gsummary.xml.groups @@ -1,17 +1,17 @@ of a column in a tab delimited file according to an expression - gsummary.py $input $out_file1 "$cond" "$groups" + +python '$__tool_directory__/gsummary.py' '$input' '$out_file1' '$cond' '$groups' + - - - - + + + - + - .. class:: warningmark This tool expects input datasets to consist of tab-delimited columns (blank or comment lines beginning with a # character are automatically skipped). @@ -33,7 +33,6 @@ This tool computes basic summary statistics on a given column, or on an expressi + **c1** *group by the values in column 1* + **c1,c4** *group by the values in column 1, then by the values in column 4* - ----- **Expression examples** @@ -52,11 +51,10 @@ This tool computes basic summary statistics on a given column, or on an expressi .. class:: infomark -**TIP:** Most functions (like *abs*) take only a single expression. *log* can take one or two parameters, like *log(expression,base)* +**TIP:** Most functions (like *abs*) take only a single expression. *log* can take one or two parameters, like *log(expression,base)* Currently, these R functions are supported: *abs, sign, sqrt, floor, ceiling, trunc, round, signif, exp, log, cos, sin, tan, acos, asin, atan, cosh, sinh, tanh, acosh, asinh, atanh, lgamma, gamma, gammaCody, digamma, trigamma, cumsum, cumprod, cummax, cummin* .. |INFO| image:: ./static/images/icon_info_sml.gif - - +