Mercurial > repos > fubar2 > abslen_bed
changeset 2:00a0c6edbbb9 draft
Uploaded
| author | fubar2 |
|---|---|
| date | Fri, 08 Dec 2023 10:14:56 +0000 |
| parents | aff6409d16d1 |
| children | df87db5eb988 |
| files | abslen_bed/.shed.yml abslen_bed/abslen_bed.python.txt abslen_bed/abslen_bed.xml abslen_bed/test-data/absin_sample abslen_bed/test-data/absout_sample absval/.shed.yml absval/absval.python.txt absval/absval.xml absval/test-data/absin_sample absval/test-data/absout_sample |
| diffstat | 8 files changed, 84 insertions(+), 73 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/abslen_bed/.shed.yml Fri Dec 08 10:14:56 2023 +0000 @@ -0,0 +1,6 @@ +category: ToolFactory generated Tools +description: ToolFactory autogenerated tool +name: abslen_bed +owner: fubar2 +synopsis: Returns a file of absolute values from differences +type: unrestricted
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/abslen_bed/abslen_bed.python.txt Fri Dec 08 10:14:56 2023 +0000 @@ -0,0 +1,14 @@ +#raw +import sys +inp = [] +for line in sys.stdin: + if line.strip() > '': + ls = line.split() + if len(ls) > 2: + x = abs(int(ls[2]) - int(ls[1])) + ls.append((str(x))) + inp.append('\t'.join(ls)) + else: + break +sys.stdout.write('\n'.join(inp)) +#end raw
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/abslen_bed/abslen_bed.xml Fri Dec 08 10:14:56 2023 +0000 @@ -0,0 +1,56 @@ +<tool name="abslen_bed" id="abslen_bed" version="1" profile="22.05"> + <!--Source in git at: https://github.com/fubar2/galaxy_tf_overlay--> + <!--Created by toolfactory@galaxy.org at 08/12/2023 08:58:50 using the Galaxy Tool Factory.--> + <description>Returns a file of absolute values from differences</description> + <requirements> + <requirement type="package">python</requirement> + </requirements> + <version_command><![CDATA[echo "1"]]></version_command> + <command><![CDATA[python +'$runme' +< +$absin +> +$absout]]></command> + <configfiles> + <configfile name="runme"><![CDATA[#raw +import sys +inp = [] +for line in sys.stdin: + if line.strip() > '': + ls = line.split() + if len(ls) > 2: + x = abs(int(ls[2]) - int(ls[1])) + ls.append((str(x))) + inp.append('\t'.join(ls)) + else: + break +sys.stdout.write('\n'.join(inp)) +#end raw]]></configfile> + </configfiles> + <inputs> + <param name="absin" type="data" optional="false" label="absin" help="Input file to be converted using abs()" format="csfasta,txt,tabular" multiple="false"/> + </inputs> + <outputs> + <data name="absout" format="txt" hidden="false"/> + </outputs> + <tests> + <test> + <param name="absin" value="absin_sample"/> + <output name="absout" value="absout_sample"/> + </test> + </tests> + <help><![CDATA[ + **What it Does** + Takes absolute values on the input + + This tool is a temporary step to enable the Sanger TreeVal NF gap_finder workflow to be + translated into Galaxy + + See https://github.com/fubar2/treeval_gal/tree/main/gap_finder + ]]></help> + <citations> + <citation type="doi">10.1093/bioinformatics/bts573</citation> + </citations> +</tool> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/abslen_bed/test-data/absin_sample Fri Dec 08 10:14:56 2023 +0000 @@ -0,0 +1,4 @@ +mm10_knownGene_uc008xda.1 900 959 +mm10_knownGene_uc008xda.1 1009 1038 +mm10_knownGene_uc008xda.1 1088 1166 +mm10_knownGene_uc008xda.1 1216 1252
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/abslen_bed/test-data/absout_sample Fri Dec 08 10:14:56 2023 +0000 @@ -0,0 +1,4 @@ +mm10_knownGene_uc008xda.1 900 959 59 +mm10_knownGene_uc008xda.1 1009 1038 29 +mm10_knownGene_uc008xda.1 1088 1166 78 +mm10_knownGene_uc008xda.1 1216 1252 36 \ No newline at end of file
--- a/absval/.shed.yml Fri Dec 08 08:47:36 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -category: ToolFactory generated Tools -description: ToolFactory autogenerated tool -name: absval -owner: fubar2 -synopsis: Returns a file of absolute values from differences -type: unrestricted
--- a/absval/absval.python.txt Fri Dec 08 08:47:36 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,11 +0,0 @@ -#raw -import sys -inp = [] -for line in sys.stdin: - if line.strip() > '': - x = line.split()[0] - inp.append(str(abs(float(x)))) - else: - break -sys.stdout.write('\n'.join(inp)) -#end raw
--- a/absval/absval.xml Fri Dec 08 08:47:36 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,56 +0,0 @@ -<tool name="absval" id="absval" version="1" profile="22.05"> - <!--Source in git at: https://github.com/fubar2/galaxy_tf_overlay--> - <!--Created by toolfactory@galaxy.org at 08/12/2023 08:31:05 using the Galaxy Tool Factory.--> - <description>Returns a file of absolute values from differences</description> - <requirements> - <requirement type="package">python</requirement> - </requirements> - <version_command><![CDATA[echo "1"]]></version_command> - <command><![CDATA[python -'$runme' -< -$absin -> -$absout]]></command> - <configfiles> - <configfile name="runme"><![CDATA[#raw -import sys -inp = [] -for line in sys.stdin: - if line.strip() > '': - ls = line.split() - if len(ls) > 2: - x = abs(int(ls[2]) - int(ls[1])) - ls.append((str(x))) - inp.append('\t'.join(ls)) - else: - break -sys.stdout.write('\n'.join(inp)) -#end raw]]></configfile> - </configfiles> - <inputs> - <param name="absin" type="data" optional="false" label="absin" help="Input file to be converted using abs()" format="csfasta,txt,tabular" multiple="false"/> - </inputs> - <outputs> - <data name="absout" format="txt" hidden="false"/> - </outputs> - <tests> - <test> - <param name="absin" value="absin_sample"/> - <output name="absout" value="absout_sample"/> - </test> - </tests> - <help><![CDATA[ - **What it Does** - Takes absolute values on the input - - This tool is a temporary step to enable the Sanger TreeVal NF gap_finder workflow to be - translated into Galaxy - - See https://github.com/fubar2/treeval_gal/tree/main/gap_finder - ]]></help> - <citations> - <citation type="doi">10.1093/bioinformatics/bts573</citation> - </citations> -</tool> -