diff --git a/tools/filters/CreateInterval.xml b/tools/filters/CreateInterval.xml index 9537b937f9e..352ea966199 100644 --- a/tools/filters/CreateInterval.xml +++ b/tools/filters/CreateInterval.xml @@ -28,19 +28,19 @@ .. class:: warningmark -**TIP**. Once your interval appears in history, you must tell Galaxy which genome it belongs to by clicking "edit attributes" link or the "?" link in the history item. +**TIP**. Once your interval appears in history, you must tell Galaxy which genome it belongs to by clicking pencil icon or the "?" link in the history item. ----- -**Syntax** +**What it does** -This tool allows you to enter a single genomic interval. The resulting history item will be in the BED format. +This tool allows you to create a single genomic interval. The resulting history item will be in the BED format. ----- **Example** -- Typing the following values in the form:: +Typing the following values in the form:: Chromosome: chrX Start position: 151087187 @@ -48,7 +48,7 @@ This tool allows you to enter a single genomic interval. The resulting history i Name: NM_000808 Strand: minus -- will create a single interval:: +will create a single interval:: chrX 151087187 151370486 NM_000808 0 - diff --git a/tools/filters/catWrapper.xml b/tools/filters/catWrapper.xml index 71aba94da6e..8c840cf77f3 100644 --- a/tools/filters/catWrapper.xml +++ b/tools/filters/catWrapper.xml @@ -23,32 +23,32 @@ ----- -**Syntax** +**What it does** -Concatenate Query2 to the end of Query1, and print on the output file. +Concatenates two queries ----- **Example** -- Query1:: +Query1:: - chrX 151087187 151087355 NM_000808_utr3_0_0_chrX_151087188_r 0 - - chrX 151572400 151572481 NM_018558_utr3_8_0_chrX_151572401_f 0 + + chrX 151087187 151087355 A 0 - + chrX 151572400 151572481 B 0 + -- Query2:: +Query2:: - chr1 151242630 151242955 NM_005416_utr3_2_0_chr1_151242631_f 0 + - chr1 151271715 151271999 NM_003125_utr3_1_0_chr1_151271716_f 0 + - chr1 151278832 151279227 NM_006945_utr3_0_0_chr1_151278833_r 0 - + chr1 151242630 151242955 X 0 + + chr1 151271715 151271999 Y 0 + + chr1 151278832 151279227 Z 0 - -- Concatenate Query2 to the end of Query1. The result is:: +The result of concatenation is:: - chrX 151087187 151087355 NM_000808_utr3_0_0_chrX_151087188_r 0 - - chrX 151572400 151572481 NM_018558_utr3_8_0_chrX_151572401_f 0 + - chr1 151242630 151242955 NM_005416_utr3_2_0_chr1_151242631_f 0 + - chr1 151271715 151271999 NM_003125_utr3_1_0_chr1_151271716_f 0 + - chr1 151278832 151279227 NM_006945_utr3_0_0_chr1_151278833_r 0 - + chrX 151087187 151087355 A 0 - + chrX 151572400 151572481 B 0 + + chr1 151242630 151242955 X 0 + + chr1 151271715 151271999 Y 0 + + chr1 151278832 151279227 Z 0 - diff --git a/tools/filters/cutWrapper.xml b/tools/filters/cutWrapper.xml index dafc9d88d06..1000e404b00 100644 --- a/tools/filters/cutWrapper.xml +++ b/tools/filters/cutWrapper.xml @@ -29,7 +29,7 @@ .. class:: warningmark -**WARNING: This tool breaks column assignments.** To re-establish column assignments run the tools and click on "edit attributes" link in the latest history item. +**WARNING: This tool breaks column assignments.** To re-establish column assignments run the tools and click on the pencil icon in the latest history item. .. class:: infomark @@ -47,9 +47,9 @@ The output of this tool is always in tabular format (e.g., if your original deli ----- -**Syntax** +**What it does** -This tool selects specified columns from the dataset. +This tool selects (cuts out) specified columns from the dataset. - Columns are specified as **c1**, **c2**, and so on. Column count begins with **1** - Columns can be specified in any order (e.g., **c2,c1,c6**) @@ -59,23 +59,23 @@ This tool selects specified columns from the dataset. **Example** -- Input dataset (six columns: c1, c2, c3, c4, c5, and c6):: +Input dataset (six columns: c1, c2, c3, c4, c5, and c6):: chr1 10 1000 gene1 0 + chr2 100 1500 gene2 0 + -- **cut** on columns "**c1,c4,c6**" will return:: +**cut** on columns "**c1,c4,c6**" will return:: chr1 gene1 + chr2 gene2 + -- **cut** on columns "**c6,c5,c4,c1**" will return:: +**cut** on columns "**c6,c5,c4,c1**" will return:: + 0 gene1 chr1 + 0 gene2 chr2 -- **cut** on columns "**c8,c7,c4**" will return:: +**cut** on columns "**c8,c7,c4**" will return:: . . gene1 . . gene2 diff --git a/tools/filters/fixedValueColumn.xml b/tools/filters/fixedValueColumn.xml index 74e31aeda7b..c45bdcfd90a 100644 --- a/tools/filters/fixedValueColumn.xml +++ b/tools/filters/fixedValueColumn.xml @@ -28,7 +28,7 @@ ----- -**Syntax** +**What it does** You can enter any value and it will be added as a new column to your Query diff --git a/tools/filters/headWrapper.xml b/tools/filters/headWrapper.xml index fa66410ee3a..0a0f2274829 100644 --- a/tools/filters/headWrapper.xml +++ b/tools/filters/headWrapper.xml @@ -2,8 +2,8 @@ lines from a Query headWrapper.pl $input $lineNum $out_file1 - - + + @@ -17,28 +17,26 @@ -**Syntax** +**What it does** -This tool output the first part of the input file. - -- **Show first** sets the number of lines to output. For example, **10** refers to output the first 10 lines of the selected query. +This tool outputs specified number of lines from the **beginning** of a dataset ----- **Example** -- Input File:: +Selecting 2 lines from this:: - chr7 56632 56652 D17003_CTCF_R6 310 + - chr7 56736 56756 D17003_CTCF_R7 354 + - chr7 56761 56781 D17003_CTCF_R4 220 + - chr7 56772 56792 D17003_CTCF_R7 372 + - chr7 56775 56795 D17003_CTCF_R4 207 + + chr7 56632 56652 D17003_CTCF_R6 310 + + chr7 56736 56756 D17003_CTCF_R7 354 + + chr7 56761 56781 D17003_CTCF_R4 220 + + chr7 56772 56792 D17003_CTCF_R7 372 + + chr7 56775 56795 D17003_CTCF_R4 207 + -- Show first 2 lines of above file. The result is:: +will produce:: - chr7 56632 56652 D17003_CTCF_R6 310 + - chr7 56736 56756 D17003_CTCF_R7 354 + + chr7 56632 56652 D17003_CTCF_R6 310 + + chr7 56736 56756 D17003_CTCF_R7 354 + diff --git a/tools/filters/pasteWrapper.xml b/tools/filters/pasteWrapper.xml index 087862adb2b..8e636dc449f 100644 --- a/tools/filters/pasteWrapper.xml +++ b/tools/filters/pasteWrapper.xml @@ -29,31 +29,31 @@ .. class:: infomark -**TIP:** Paste preserves column assignments of Query1 +Paste preserves column assignments of the first dataset ----- -**Syntax** +**What it does** -This tool merges two queries side by side. If the first (left) query contains column assignments such as chromosome, start, end and strand, these will be preserved. However, if you would like to change column assignments, use "edit attributes" link in the history item. +This tool merges two datasets side by side. If the first (left) query contains column assignments such as chromosome, start, end and strand, these will be preserved. However, if you would like to change column assignments, click the pencil icon in the history item. ----- **Example** -- Query 1:: +First dataset:: a 1 a 2 a 3 -- Query 2:: +Second dataset:: 20 30 40 -- Pasting them together will produce:: +Pasting them together will produce:: a 1 20 a 2 30 diff --git a/tools/filters/remove_beginning.xml b/tools/filters/remove_beginning.xml index daadc14bed1..3ba8d5cb59c 100644 --- a/tools/filters/remove_beginning.xml +++ b/tools/filters/remove_beginning.xml @@ -2,8 +2,8 @@ of a file remove_beginning.pl $input $num_lines $out_file1 - - + + @@ -17,28 +17,26 @@ -**Syntax** +**What it does** -This tool removes the specified number of lines from the beginning of the file - -- **Remove first** specifies the number of lines from the beginning of the file to remove. For example, 10 refers to remove the first 10 lines of the selected query. +This tool removes specified number of lines from the beginning of a dataset ----- **Example** -- Input File:: +Input File:: - chr7 56632 56652 D17003_CTCF_R6 310 + - chr7 56736 56756 D17003_CTCF_R7 354 + - chr7 56761 56781 D17003_CTCF_R4 220 + - chr7 56772 56792 D17003_CTCF_R7 372 + - chr7 56775 56795 D17003_CTCF_R4 207 + + chr7 56632 56652 D17003_CTCF_R6 310 + + chr7 56736 56756 D17003_CTCF_R7 354 + + chr7 56761 56781 D17003_CTCF_R4 220 + + chr7 56772 56792 D17003_CTCF_R7 372 + + chr7 56775 56795 D17003_CTCF_R4 207 + -- Remove the first 3 lines of the above file. The result is:: +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 + + 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 515c12409a2..59349693e5e 100644 --- a/tools/filters/tailWrapper.xml +++ b/tools/filters/tailWrapper.xml @@ -2,8 +2,8 @@ lines from a Query tailWrapper.pl $input $lineNum $out_file1 - - + + @@ -17,11 +17,9 @@ -**Syntax** +**What it does** -This tool output the last part of the input file. - -- **Show last** sets the number of lines to output. For example, **10** refers to output the last 10 lines of the selected query. +This tool outputs specified number of lines from the **end** of a dataset ----- diff --git a/tools/stats/column_maker.xml b/tools/stats/column_maker.xml index f97602c122a..befee863d52 100644 --- a/tools/stats/column_maker.xml +++ b/tools/stats/column_maker.xml @@ -32,7 +32,7 @@ ----- -**Syntax** +**What it does** This tool computes an expression for every row of a query and appends the result as a new column (field). @@ -44,30 +44,30 @@ This tool computes an expression for every row of a query and appends the result **Example** -- Input file:: +If this is your input:: - chr1 151077881 151077918 2 200 - - chr1 151081985 151082078 3 500 + + chr1 151077881 151077918 2 200 - + chr1 151081985 151082078 3 500 + -- Using Input file, compute "c4*c5" results in:: +computing "c4*c5" will produce:: - chr1 151077881 151077918 2 200 - 400.0 - chr1 151081985 151082078 3 500 + 1500.0 + chr1 151077881 151077918 2 200 - 400.0 + chr1 151081985 151082078 3 500 + 1500.0 -- If "Round result?" is YES, compute "c4*c5" results in:: +if, at the same time, "Round result?" is set to **YES** results will look like this:: - chr1 151077881 151077918 2 200 - 400 - chr1 151081985 151082078 3 500 + 1500 + chr1 151077881 151077918 2 200 - 400 + chr1 151081985 151082078 3 500 + 1500 -- Many operations are functional. For example, compute "c3>=c2" for Input file results in:: +You can also use this tool to evaluate expressions. For example, computing "c3>=c2" for Input will result in the following:: - chr1 151077881 151077918 2 200 - True - chr1 151081985 151082078 3 500 + True + chr1 151077881 151077918 2 200 - True + chr1 151081985 151082078 3 500 + True -- Another example, compute "type(c2)==type('') for Input file resutls in:: +or computing "type(c2)==type('') for Input will return:: - chr1 151077881 151077918 2 200 - False - chr1 151081985 151082078 3 500 + False + chr1 151077881 151077918 2 200 - False + chr1 151081985 151082078 3 500 + False